diff --git a/Snakefile b/Snakefile index 2728412..d60bc20 100755 --- a/Snakefile +++ b/Snakefile @@ -18,7 +18,7 @@ rule all: rule files: params: dropped_strains = "config/dropped_strains_{subtype}.txt", - include_strains = "config/include_strains_{subtype}.txt", + include_strains = "config/include_strains_{subtype}_{time}.txt", reference = "config/reference_{subtype}_{segment}.gb", colors = "config/colors_{subtype}.tsv", lat_longs = "config/lat_longs_{subtype}.tsv", diff --git a/config/auspice_config_h5nx-2-year.json b/config/auspice_config_h5nx-2-year.json deleted file mode 100755 index 0ae2b0d..0000000 --- a/config/auspice_config_h5nx-2-year.json +++ /dev/null @@ -1,108 +0,0 @@ -{ - "title": "Real-time tracking of influenza A/H5NX virus evolution", - "maintainers": [ - {"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"} - ], - "build_url": "https://github.com/nextstrain/avian-flu", - "data_provenance": [ - { - "name": "GISAID" - } - ], - "colorings": [ - { - "key": "gt", - "title": "Genotype", - "type": "categorical" - }, - { - "key": "num_date", - "title": "Date", - "type": "continuous" - }, - { - "key": "country", - "title": "Country", - "type": "categorical" - }, - { - "key": "region", - "title": "Region", - "type": "categorical" - }, - { - "key": "host", - "title": "Host", - "type": "categorical" - }, - { - "key": "domestic_status", - "title": "Domestic or Wild", - "type": "categorical" - }, - { - "key": "subtype", - "title": "Subtype", - "type": "categorical" - }, - { - "key": "h5_label_clade", - "title": "Provisional LABEL clade", - "type": "categorical" - }, - { - "key": "gisaid_clade", - "title": "GISAID clade", - "type": "categorical" - }, - { - "key": "furin_cleavage_motif", - "title": "furin cleavage motif", - "type": "categorical" - }, - { - "key": "cleavage_site_sequence", - "title": "cleavage site sequence", - "type": "categorical" - }, - { - "key": "authors", - "title": "Authors", - "type": "categorical" - }, - { - "key": "PMID", - "title": "Pubmed ID", - "type": "categorical" - }, - { - "key": "submitting_lab", - "title": "Submitting lab", - "type": "categorical" - }, - { - "key": "originating_lab", - "title": "Originating lab", - "type": "categorical" - } - ], - "geo_resolutions": [ - "region", - "country" - ], - "display_defaults": { - "map_triplicate": true, - "color_by": "region" - }, - "filters": [ - "host", - "domestic_status", - "region", - "country", - "submitting_lab", - "subtype", - "h5_label_clade", - "gisaid_clade", - "authors" - ] -} diff --git a/config/auspice_config_h5nx-all-time.json b/config/auspice_config_h5nx-all-time.json deleted file mode 100755 index 0ae2b0d..0000000 --- a/config/auspice_config_h5nx-all-time.json +++ /dev/null @@ -1,108 +0,0 @@ -{ - "title": "Real-time tracking of influenza A/H5NX virus evolution", - "maintainers": [ - {"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"} - ], - "build_url": "https://github.com/nextstrain/avian-flu", - "data_provenance": [ - { - "name": "GISAID" - } - ], - "colorings": [ - { - "key": "gt", - "title": "Genotype", - "type": "categorical" - }, - { - "key": "num_date", - "title": "Date", - "type": "continuous" - }, - { - "key": "country", - "title": "Country", - "type": "categorical" - }, - { - "key": "region", - "title": "Region", - "type": "categorical" - }, - { - "key": "host", - "title": "Host", - "type": "categorical" - }, - { - "key": "domestic_status", - "title": "Domestic or Wild", - "type": "categorical" - }, - { - "key": "subtype", - "title": "Subtype", - "type": "categorical" - }, - { - "key": "h5_label_clade", - "title": "Provisional LABEL clade", - "type": "categorical" - }, - { - "key": "gisaid_clade", - "title": "GISAID clade", - "type": "categorical" - }, - { - "key": "furin_cleavage_motif", - "title": "furin cleavage motif", - "type": "categorical" - }, - { - "key": "cleavage_site_sequence", - "title": "cleavage site sequence", - "type": "categorical" - }, - { - "key": "authors", - "title": "Authors", - "type": "categorical" - }, - { - "key": "PMID", - "title": "Pubmed ID", - "type": "categorical" - }, - { - "key": "submitting_lab", - "title": "Submitting lab", - "type": "categorical" - }, - { - "key": "originating_lab", - "title": "Originating lab", - "type": "categorical" - } - ], - "geo_resolutions": [ - "region", - "country" - ], - "display_defaults": { - "map_triplicate": true, - "color_by": "region" - }, - "filters": [ - "host", - "domestic_status", - "region", - "country", - "submitting_lab", - "subtype", - "h5_label_clade", - "gisaid_clade", - "authors" - ] -} diff --git a/config/colors_h5nx-2-year.tsv b/config/colors_h5nx-2-year.tsv deleted file mode 100755 index e5dbdaa..0000000 --- a/config/colors_h5nx-2-year.tsv +++ /dev/null @@ -1,149 +0,0 @@ -region antarctica #213A67 -region china #4042C7 -region southeast_asia #4274CE -region southeast asia #4274CE -region south_asia #5199B7 -region south asia #5199B7 -region japan_korea #69B091 -region japan korea #69B091 -region oceania #88BB6C -region west_asia #ADBD51 -region west asia #ADBD51 -region africa #CEB541 -region europe #E39B39 -region south_america #E56C2F -region south america #E56C2F -region north_america #DC2F24 -region north america #DC2F24 -subtype h5n1 #4274CE -subtype h5n2 #E39B39 -subtype h5n3 #4042C7 -subtype h5n4 #E56C2F -subtype h5n5 #88BB6C -subtype h5n6 #CEB541 -subtype h5n7 #ADBD51 -subtype h5n8 #69B091 -subtype h5n9 #DC2F24 -host avian #4066CF -host environment #77B67F -host nonhuman mammal #CEB541 -host human #DC2F24 -h5_label_clade 0 #290F54 -h5_label_clade 1 #3D167E -h5_label_clade 1-8-9-like #3D167E -h5_label_clade 1.1 #521EA7 -h5_label_clade 1.1-like #521EA7 -h5_label_clade 1.1.1 #5E1D9D -h5_label_clade 1.1.2 #4C24B0 -h5_label_clade 2-like #4C24B0 -h5_label_clade 2.1.1 #472DB8 -h5_label_clade 2.1.2 #4335C0 -h5_label_clade 2.1.3 #403EC6 -h5_label_clade 2.1.3.1 #403EC6 -h5_label_clade 2.1.3.2 #3F48C9 -h5_label_clade 2.1.3.2a #3F53CD -h5_label_clade 2.1.3.2b #3E5DD0 -h5_label_clade 2.1.3.3 #4066CF -h5_label_clade 2.2 #4270CE -h5_label_clade 2.2.1 #4379CD -h5_label_clade 2.2.1.1 #4682C9 -h5_label_clade 2.2.1.1a #4989C4 -h5_label_clade 2.2.1.2 #4C91C0 -h5_label_clade 2.2.2 #5097BA -h5_label_clade 2.2.2.1 #549DB3 -h5_label_clade 2.3.1 #58A2AC -h5_label_clade 2.3.2 #5CA7A5 -h5_label_clade 2.3.2.1 #61AB9D -h5_label_clade 2.3.2.1a #67AE95 -h5_label_clade 2.3.2.1b #6CB28D -h5_label_clade 2.3.2.1c #72B485 -h5_label_clade 2.3.2.1c-like #78B77D -h5_label_clade 2.3.2.1d #7FB976 -h5_label_clade 2.3.2.1e #85BA6E -h5_label_clade 2.3.2.1f #85BA6E -h5_label_clade 2.3.2.1g #8CBB68 -h5_label_clade 2.3.3 #93BD62 -h5_label_clade 2.3.4 #93BD62 -h5_label_clade 2.3.4-like #9BBE5C -h5_label_clade 2.3.4.1 #A2BE57 -h5_label_clade 2.3.4.2 #A9BD53 -h5_label_clade 2.3.4.3 #A9BD53 -h5_label_clade 2.3.4.4 #B1BD4E -h5_label_clade 2.3.4.4-like #B8BC4B -h5_label_clade 2.3.4.4a #BFBB48 -h5_label_clade 2.3.4.4b #C5B945 -h5_label_clade 2.3.4.4b #C5B945 -h5_label_clade 2.3.4.4c #CCB742 -h5_label_clade 2.3.4.4d #D1B340 -h5_label_clade 2.3.4.4e #D6AF3E -h5_label_clade 2.3.4.4f #DCAB3D -h5_label_clade 2.3.4.4g #DFA53B -h5_label_clade 2.3.4.4h #E29E39 -h5_label_clade 2.4 #E49838 -h5_label_clade 2.5 #E68F36 -h5_label_clade 3 #E68634 -h5_label_clade 3-like #E67C33 -h5_label_clade 4 #E67231 -h5_label_clade 5 #E4652E -h5_label_clade 5-6-like #E4652E -h5_label_clade 6 #E2592C -h5_label_clade 7 #E04D29 -h5_label_clade 7.1 #E04D29 -h5_label_clade 7.2 #E04D29 -h5_label_clade 8 #E04D29 -h5_label_clade 8-9-like #DF4127 -h5_label_clade 9 #DF4127 -h5_label_clade EA-nonGsGD #DD3425 -h5_label_clade Am-nonGsGD #891916 -gisaid_clade 0 #5E1D9D -gisaid_clade 1 #521EA7 -gisaid_clade 1-8-9-like #4C24B0 -gisaid_clade 1.1 #472DB8 -gisaid_clade 1.1-like #4335C0 -gisaid_clade 1.1.1 #403EC6 -gisaid_clade 1.1.2 #3F48C9 -gisaid_clade 2.1.1 #3F53CD -gisaid_clade 2.1.2 #3E5DD0 -gisaid_clade 2.1.3 #4066CF -gisaid_clade 2.1.3.1 #4270CE -gisaid_clade 2.1.3.2 #4379CD -gisaid_clade 2.1.3.2a #4682C9 -gisaid_clade 2.1.3.2b #4989C4 -gisaid_clade 2.1.3.3 #4C91C0 -gisaid_clade 2.2 #5097BA -gisaid_clade 2.2.1 #549DB3 -gisaid_clade 2.2.1.1 #58A2AC -gisaid_clade 2.2.1.1a #5CA7A5 -gisaid_clade 2.2.1.2 #61AB9D -gisaid_clade 2.2.2 #67AE95 -gisaid_clade 2.2.2.1 #6CB28D -gisaid_clade 2.3.1 #72B485 -gisaid_clade 2.3.2 #78B77D -gisaid_clade 2.3.2.1 #7FB976 -gisaid_clade 2.3.2.1a #85BA6E -gisaid_clade 2.3.2.1b #8CBB68 -gisaid_clade 2.3.2.1c #93BD62 -gisaid_clade 2.3.3 #9BBE5C -gisaid_clade 2.3.4 #A2BE57 -gisaid_clade 2.3.4-like #A9BD53 -gisaid_clade 2.3.4.1 #B1BD4E -gisaid_clade 2.3.4.2 #B8BC4B -gisaid_clade 2.3.4.3 #BFBB48 -gisaid_clade 2.3.4.4 #C5B945 -gisaid_clade 2.3.4.4b #CCB742 -gisaid_clade 2.3.4.4c #D1B340 -gisaid_clade 2.3.4.4g #D6AF3E -gisaid_clade 2.3.4.4e #DCAB3D -gisaid_clade 2.3.4.4h #DFA53B -gisaid_clade 2.5 #E29E39 -gisaid_clade 3 #E49838 -gisaid_clade 4 #E68F36 -gisaid_clade 5 #E68634 -gisaid_clade 6 #E67C33 -gisaid_clade 7 #E67231 -gisaid_clade 7.1 #E4652E -gisaid_clade 7.2 #E2592C -gisaid_clade 8 #E04D29 -gisaid_clade 9 #DF4127 -gisaid_clade EA_nonGsGD #DD3425 -gisaid_clade Am_nonGsGD #891916 diff --git a/config/colors_h5nx-all-time.tsv b/config/colors_h5nx-all-time.tsv deleted file mode 100755 index e5dbdaa..0000000 --- a/config/colors_h5nx-all-time.tsv +++ /dev/null @@ -1,149 +0,0 @@ -region antarctica #213A67 -region china #4042C7 -region southeast_asia #4274CE -region southeast asia #4274CE -region south_asia #5199B7 -region south asia #5199B7 -region japan_korea #69B091 -region japan korea #69B091 -region oceania #88BB6C -region west_asia #ADBD51 -region west asia #ADBD51 -region africa #CEB541 -region europe #E39B39 -region south_america #E56C2F -region south america #E56C2F -region north_america #DC2F24 -region north america #DC2F24 -subtype h5n1 #4274CE -subtype h5n2 #E39B39 -subtype h5n3 #4042C7 -subtype h5n4 #E56C2F -subtype h5n5 #88BB6C -subtype h5n6 #CEB541 -subtype h5n7 #ADBD51 -subtype h5n8 #69B091 -subtype h5n9 #DC2F24 -host avian #4066CF -host environment #77B67F -host nonhuman mammal #CEB541 -host human #DC2F24 -h5_label_clade 0 #290F54 -h5_label_clade 1 #3D167E -h5_label_clade 1-8-9-like #3D167E -h5_label_clade 1.1 #521EA7 -h5_label_clade 1.1-like #521EA7 -h5_label_clade 1.1.1 #5E1D9D -h5_label_clade 1.1.2 #4C24B0 -h5_label_clade 2-like #4C24B0 -h5_label_clade 2.1.1 #472DB8 -h5_label_clade 2.1.2 #4335C0 -h5_label_clade 2.1.3 #403EC6 -h5_label_clade 2.1.3.1 #403EC6 -h5_label_clade 2.1.3.2 #3F48C9 -h5_label_clade 2.1.3.2a #3F53CD -h5_label_clade 2.1.3.2b #3E5DD0 -h5_label_clade 2.1.3.3 #4066CF -h5_label_clade 2.2 #4270CE -h5_label_clade 2.2.1 #4379CD -h5_label_clade 2.2.1.1 #4682C9 -h5_label_clade 2.2.1.1a #4989C4 -h5_label_clade 2.2.1.2 #4C91C0 -h5_label_clade 2.2.2 #5097BA -h5_label_clade 2.2.2.1 #549DB3 -h5_label_clade 2.3.1 #58A2AC -h5_label_clade 2.3.2 #5CA7A5 -h5_label_clade 2.3.2.1 #61AB9D -h5_label_clade 2.3.2.1a #67AE95 -h5_label_clade 2.3.2.1b #6CB28D -h5_label_clade 2.3.2.1c #72B485 -h5_label_clade 2.3.2.1c-like #78B77D -h5_label_clade 2.3.2.1d #7FB976 -h5_label_clade 2.3.2.1e #85BA6E -h5_label_clade 2.3.2.1f #85BA6E -h5_label_clade 2.3.2.1g #8CBB68 -h5_label_clade 2.3.3 #93BD62 -h5_label_clade 2.3.4 #93BD62 -h5_label_clade 2.3.4-like #9BBE5C -h5_label_clade 2.3.4.1 #A2BE57 -h5_label_clade 2.3.4.2 #A9BD53 -h5_label_clade 2.3.4.3 #A9BD53 -h5_label_clade 2.3.4.4 #B1BD4E -h5_label_clade 2.3.4.4-like #B8BC4B -h5_label_clade 2.3.4.4a #BFBB48 -h5_label_clade 2.3.4.4b #C5B945 -h5_label_clade 2.3.4.4b #C5B945 -h5_label_clade 2.3.4.4c #CCB742 -h5_label_clade 2.3.4.4d #D1B340 -h5_label_clade 2.3.4.4e #D6AF3E -h5_label_clade 2.3.4.4f #DCAB3D -h5_label_clade 2.3.4.4g #DFA53B -h5_label_clade 2.3.4.4h #E29E39 -h5_label_clade 2.4 #E49838 -h5_label_clade 2.5 #E68F36 -h5_label_clade 3 #E68634 -h5_label_clade 3-like #E67C33 -h5_label_clade 4 #E67231 -h5_label_clade 5 #E4652E -h5_label_clade 5-6-like #E4652E -h5_label_clade 6 #E2592C -h5_label_clade 7 #E04D29 -h5_label_clade 7.1 #E04D29 -h5_label_clade 7.2 #E04D29 -h5_label_clade 8 #E04D29 -h5_label_clade 8-9-like #DF4127 -h5_label_clade 9 #DF4127 -h5_label_clade EA-nonGsGD #DD3425 -h5_label_clade Am-nonGsGD #891916 -gisaid_clade 0 #5E1D9D -gisaid_clade 1 #521EA7 -gisaid_clade 1-8-9-like #4C24B0 -gisaid_clade 1.1 #472DB8 -gisaid_clade 1.1-like #4335C0 -gisaid_clade 1.1.1 #403EC6 -gisaid_clade 1.1.2 #3F48C9 -gisaid_clade 2.1.1 #3F53CD -gisaid_clade 2.1.2 #3E5DD0 -gisaid_clade 2.1.3 #4066CF -gisaid_clade 2.1.3.1 #4270CE -gisaid_clade 2.1.3.2 #4379CD -gisaid_clade 2.1.3.2a #4682C9 -gisaid_clade 2.1.3.2b #4989C4 -gisaid_clade 2.1.3.3 #4C91C0 -gisaid_clade 2.2 #5097BA -gisaid_clade 2.2.1 #549DB3 -gisaid_clade 2.2.1.1 #58A2AC -gisaid_clade 2.2.1.1a #5CA7A5 -gisaid_clade 2.2.1.2 #61AB9D -gisaid_clade 2.2.2 #67AE95 -gisaid_clade 2.2.2.1 #6CB28D -gisaid_clade 2.3.1 #72B485 -gisaid_clade 2.3.2 #78B77D -gisaid_clade 2.3.2.1 #7FB976 -gisaid_clade 2.3.2.1a #85BA6E -gisaid_clade 2.3.2.1b #8CBB68 -gisaid_clade 2.3.2.1c #93BD62 -gisaid_clade 2.3.3 #9BBE5C -gisaid_clade 2.3.4 #A2BE57 -gisaid_clade 2.3.4-like #A9BD53 -gisaid_clade 2.3.4.1 #B1BD4E -gisaid_clade 2.3.4.2 #B8BC4B -gisaid_clade 2.3.4.3 #BFBB48 -gisaid_clade 2.3.4.4 #C5B945 -gisaid_clade 2.3.4.4b #CCB742 -gisaid_clade 2.3.4.4c #D1B340 -gisaid_clade 2.3.4.4g #D6AF3E -gisaid_clade 2.3.4.4e #DCAB3D -gisaid_clade 2.3.4.4h #DFA53B -gisaid_clade 2.5 #E29E39 -gisaid_clade 3 #E49838 -gisaid_clade 4 #E68F36 -gisaid_clade 5 #E68634 -gisaid_clade 6 #E67C33 -gisaid_clade 7 #E67231 -gisaid_clade 7.1 #E4652E -gisaid_clade 7.2 #E2592C -gisaid_clade 8 #E04D29 -gisaid_clade 9 #DF4127 -gisaid_clade EA_nonGsGD #DD3425 -gisaid_clade Am_nonGsGD #891916 diff --git a/config/dropped_strains_h5n1.txt b/config/dropped_strains_h5n1.txt index 2f5eac8..d571e15 100755 --- a/config/dropped_strains_h5n1.txt +++ b/config/dropped_strains_h5n1.txt @@ -5,3 +5,4 @@ A/mink/EasternChina/0712/2018 # divergent A/chicken/Dakahlia/110/2007 # divergent A/chicken/Pessel/BPPVRII/2007 # divergent A/duck/China/E26/2012 # divergent +A/Fox/Bayern/WS113/2022 diff --git a/config/dropped_strains_h5nx-2-year.txt b/config/dropped_strains_h5nx-2-year.txt deleted file mode 100755 index b9305f9..0000000 --- a/config/dropped_strains_h5nx-2-year.txt +++ /dev/null @@ -1,22 +0,0 @@ -A/chicken/Scotland/1959 -A/mallard/Poland/141/2015 # overly divergent -A/duck/Vietnam/1151/2014 # very divergent -A/aquaticbird/Korea/w209/2007 # very divergent -A/swine/Korea/C13/2008 # very divergent -A/wildbirdfeces/Korea/H2262/2015 # very divergent -A/chicken/Taiwan/A1/2019 -A/Chicken/Egypt/AR528/2017 -A/Avian/Iran/38AMA/2019 -A/chicken/Aguascalientes/IA13/2010 -A/duck/Hunan/0307YYGK1L3OC/2018 -A/chicken/Coahuila/IA05/2009 -A/mink/EasternChina/0712/2018 -A/laughinggull/DelawareBay/486/2018 -A/goose/Fujian/1123FZHX0009O/2017 -A/duck/EasternChina/S0131/2014 -A/duck/China/E26/2012 -A/chicken/Zhejiang/217/2016 -A/duck/Hunan/1207YYGK111P/2013 -A/chicken/Dakahlia/110/2007 # divergent -A/chicken/Pessel/BPPVRII/2007 # divergent -A/duck/China/E26/2012 # divergent \ No newline at end of file diff --git a/config/dropped_strains_h5nx-all-time.txt b/config/dropped_strains_h5nx-all-time.txt deleted file mode 100755 index b9305f9..0000000 --- a/config/dropped_strains_h5nx-all-time.txt +++ /dev/null @@ -1,22 +0,0 @@ -A/chicken/Scotland/1959 -A/mallard/Poland/141/2015 # overly divergent -A/duck/Vietnam/1151/2014 # very divergent -A/aquaticbird/Korea/w209/2007 # very divergent -A/swine/Korea/C13/2008 # very divergent -A/wildbirdfeces/Korea/H2262/2015 # very divergent -A/chicken/Taiwan/A1/2019 -A/Chicken/Egypt/AR528/2017 -A/Avian/Iran/38AMA/2019 -A/chicken/Aguascalientes/IA13/2010 -A/duck/Hunan/0307YYGK1L3OC/2018 -A/chicken/Coahuila/IA05/2009 -A/mink/EasternChina/0712/2018 -A/laughinggull/DelawareBay/486/2018 -A/goose/Fujian/1123FZHX0009O/2017 -A/duck/EasternChina/S0131/2014 -A/duck/China/E26/2012 -A/chicken/Zhejiang/217/2016 -A/duck/Hunan/1207YYGK111P/2013 -A/chicken/Dakahlia/110/2007 # divergent -A/chicken/Pessel/BPPVRII/2007 # divergent -A/duck/China/E26/2012 # divergent \ No newline at end of file diff --git a/config/dropped_strains_h5nx.txt b/config/dropped_strains_h5nx.txt index b9305f9..5123e4f 100755 --- a/config/dropped_strains_h5nx.txt +++ b/config/dropped_strains_h5nx.txt @@ -19,4 +19,5 @@ A/chicken/Zhejiang/217/2016 A/duck/Hunan/1207YYGK111P/2013 A/chicken/Dakahlia/110/2007 # divergent A/chicken/Pessel/BPPVRII/2007 # divergent -A/duck/China/E26/2012 # divergent \ No newline at end of file +A/duck/China/E26/2012 # divergent +A/Fox/Bayern/WS113/2022 \ No newline at end of file diff --git a/config/include_strains_h5n1_2y.txt b/config/include_strains_h5n1_2y.txt new file mode 100755 index 0000000..1afb37c --- /dev/null +++ b/config/include_strains_h5n1_2y.txt @@ -0,0 +1,38 @@ +A/Colorado/18/2022 +A/England/215201407/2021 +A/Astrakhan/3212/2020 +A/Mink/Spain/3691822VIR1058610/2022 +A/Mink/Spain/3691222VIR105868/2022 +A/Mink/Spain/36911022VIR1058611/2022 +A/mink/Spain/22VIR127741438693/2022 +A/mink/Spain/22VIR127741338692/2022 +A/Mink/Spain/3691322VIR105869/2022 +A/Cambodia/NPH230032/2023 +A/domesticcat/Poland/Kot1/2023 +A/domesticcat/Poland/H254/2023 +A/domesticcat/Poland/H252/2023 +A/domesticcat/Poland/H249/2023 +A/domesticcat/Poland/H253/2023 +A/domesticcat/Poland/H248/2023 +A/domesticcat/Poland/H247/2023 +A/dairycattle/Texas/24008749001original/2024 +A/dairycattle/Texas/24008749003original/2024 +A/dairycattle/Texas/24008749004original/2024 +A/dairycattle/Texas/24008749006original/2024 +A/dairycattle/Texas/24008749007original/2024 +A/dairycattle/Texas/24008749005original/2024 +A/dairycattle/Texas/24008749002v/2024 +A/goat/Minnesota/24007234006original/2024 +A/goat/Minnesota/24007234009original/2024 +A/goat/Minnesota/24007234003original/2024 +A/Texas/37/2024 +A/feline/USA/24009116005original/2024 +A/feline/USA/24008850001original/2024 +A/feline/USA/24009116004original/2024 +A/feline/USA/24009116002original/2024 +A/feline/USA/24008764001original/2024 +A/feline/USA/24009311006original/2024 +A/feline/USA/24008764002original/2024 +A/feline/USA/23037332001original/2023 +A/feline/USA/24008850002original/2024 +A/feline/USA/24009311004original/2024 diff --git a/config/include_strains_h5n1.txt b/config/include_strains_h5n1_all-time.txt similarity index 100% rename from config/include_strains_h5n1.txt rename to config/include_strains_h5n1_all-time.txt diff --git a/config/include_strains_h5nx-2-year.txt b/config/include_strains_h5nx_2y.txt similarity index 100% rename from config/include_strains_h5nx-2-year.txt rename to config/include_strains_h5nx_2y.txt diff --git a/config/include_strains_h5nx-all-time.txt b/config/include_strains_h5nx_all-time.txt similarity index 100% rename from config/include_strains_h5nx-all-time.txt rename to config/include_strains_h5nx_all-time.txt diff --git a/config/include_strains_h7n9.txt b/config/include_strains_h7n9_all-time.txt similarity index 100% rename from config/include_strains_h7n9.txt rename to config/include_strains_h7n9_all-time.txt diff --git a/config/include_strains_h9n2.txt b/config/include_strains_h9n2_all-time.txt similarity index 100% rename from config/include_strains_h9n2.txt rename to config/include_strains_h9n2_all-time.txt diff --git a/config/lat_longs_h5nx-2-year.tsv b/config/lat_longs_h5nx-2-year.tsv deleted file mode 100755 index 3f73c14..0000000 --- a/config/lat_longs_h5nx-2-year.tsv +++ /dev/null @@ -1,6 +0,0 @@ -country tibet 31.129337 88.671049 -country antarctica -69.6354154 0.0 -region antarctica -69.6354154 0.0 -country namibia -22.967062 18.4929993 -country democraticrepublicofcongo -4.0335162 21.7500603 -country greenland 71.7069 42.6043 diff --git a/config/lat_longs_h5nx-all-time.tsv b/config/lat_longs_h5nx-all-time.tsv deleted file mode 100755 index 3f73c14..0000000 --- a/config/lat_longs_h5nx-all-time.tsv +++ /dev/null @@ -1,6 +0,0 @@ -country tibet 31.129337 88.671049 -country antarctica -69.6354154 0.0 -region antarctica -69.6354154 0.0 -country namibia -22.967062 18.4929993 -country democraticrepublicofcongo -4.0335162 21.7500603 -country greenland 71.7069 42.6043 diff --git a/config/reference_h5nx-2-year_ha.gb b/config/reference_h5nx-2-year_ha.gb deleted file mode 100644 index 66bbb01..0000000 --- a/config/reference_h5nx-2-year_ha.gb +++ /dev/null @@ -1,94 +0,0 @@ -LOCUS OL638145 1742 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 4 hemagglutinin (HA) gene, complete cds. -ACCESSION OL638145 -VERSION OL638145.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 1742) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..1742 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="4" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 15..1718 - /gene="HA" - CDS 15..1718 - /gene="HA" - /function="receptor binding and fusion protein" - /codon_start=1 - /product="hemagglutinin" - /protein_id="UFL16554.1" - /translation="MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTH - AQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPA - NDLCYPGSLNDYEELKHLLSRINHFEKILIIPKSSWPNHETSLGVSAACPYQGAPSFF - RNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPTTYISVGT - STLNQRLVPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKG - DSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLR - NSPLREKRRKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDG - VTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENE - RTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYS - EEARLKREEISGVKLESIGTYQILSIYSTAASSLALAIMMAGLSLWMCSNGSLQCRIC - I" - sig_peptide 15..62 - /gene="HA" - mat_peptide 63..1049 - /gene="HA" - /product="HA1" - mat_peptide 1050..1715 - /gene="HA" - /product="HA2" -ORIGIN - 1 ttcactctgt caaaatggag aacatagtac ttcttcttgc aatagttagc cttgttaaaa - 61 gtgatcagat ttgcattggt taccatgcaa acaattcgac agagcaagtt gacacgataa - 121 tggaaaagaa cgtcactgtt acacatgccc aagacatact ggaaaaaaca cacaacggga - 181 agctctgtga tctaaatggg gtgaagcctc tgattttaaa ggattgtagt gtagctggat - 241 ggctcctcgg aaacccaatg tgcgacgaat tcatcagagt gccggaatgg tcctacatag - 301 tggagcgggc taatccagct aatgacctct gttacccagg gagcctcaat gactatgaag - 361 aactgaaaca cctgttgagc agaataaatc attttgagaa gattctgatc atccccaaga - 421 gttcctggcc aaatcatgaa acatcactag gggtgagcgc agcttgtcca taccagggag - 481 cgccctcctt tttcagaaat gtggtgtggc ttatcaaaaa gaacgatgca tacccaacaa - 541 taaagataag ctacaataat accaatcggg aagatctctt gatattgtgg gggattcatc - 601 attccaacaa tgcagaagag cagacaaatc tctacaaaaa cccaaccacc tatatttcag - 661 ttggaacatc aactttaaac cagaggttgg taccaaaaat agctactaga tcccaagtaa - 721 acgggcaacg tggaagaatg gacttcttct ggacaatttt aaaaccagat gatgcaatcc - 781 atttcgagag taatggaaat ttcattgctc cagagtatgc atacaaaatt gtcaagaaag - 841 gggactcaac aattatgaaa agtggagtgg aatatggcca ctgcaacacc aaatgtcaaa - 901 ccccagtagg agcgataaat tctagtatgc cattccacaa catacatcct ctcaccattg - 961 gggaatgccc caaatacgtg aagtcaaaca agttggtcct tgcgactggg cttagaaata - 1021 gtcctctaag agaaaagaga agaaaaagag gcctgtttgg ggcgatagca gggtttatag - 1081 agggaggatg gcagggaatg gttgatggtt ggtatgggta ccatcatagc aatgagcagg - 1141 ggagtgggta cgctgcagac aaagaatcca cccagaaggc aatagatgga gttaccaata - 1201 aggtcaactc aatcattgac aaaatgaaca ctcaatttga ggcagttgga agggagttta - 1261 ataacttaga aaggaggata gagaatttga acaagaaaat ggaagacgga ttcctagatg - 1321 tctggaccta taatgctgaa cttctagttc tcatggaaaa cgagaggact ctagatttcc - 1381 atgattcaaa tgtcaagaac ctttacgaca aagtcagact acagcttagg gataatgcaa - 1441 aggagctggg taacggctgt ttcgaattct atcacaaatg cgataatgaa tgtatggaaa - 1501 gtgtgagaaa tgggacgtat gactaccctc agtattcaga agaagcaaga ttaaaaagag - 1561 aagaaataag cggagtgaaa ttagaatcaa taggaactta ccagatactg tcaatttatt - 1621 caacagcggc aagttcccta gcactggcaa tcatgatggc tggtctatct ttatggatgt - 1681 gctccaatgg gtcgttacag tgcagaattt gcatttagat ttgtgagctc agattgtagt - 1741 ta -// - diff --git a/config/reference_h5nx-2-year_mp.gb b/config/reference_h5nx-2-year_mp.gb deleted file mode 100644 index 0281df6..0000000 --- a/config/reference_h5nx-2-year_mp.gb +++ /dev/null @@ -1,76 +0,0 @@ -LOCUS OL638146 982 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 7 matrix protein 2 (M2) gene, partial cds; and matrix - protein 1 (M1) gene, complete cds. -ACCESSION OL638146 -VERSION OL638146.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 982) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..982 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="7" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 2..>982 - /gene="M2" - CDS join(2..27,716..>982) - /gene="M2" - /codon_start=1 - /product="matrix protein 2" - /protein_id="UFL16556.1" - /translation="MSLLTEVETPTKNGWECNCSDSSDPLVIAASIIGILHLILWILD - RLFFKCVYRRLKYGLKRGPSTEGVPESMREEYRQEQQSAVDVDDGHFVNIELE" - gene 2..760 - /gene="M1" - CDS 2..760 - /gene="M1" - /codon_start=1 - /product="matrix protein 1" - /protein_id="UFL16555.1" - /translation="MSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEALME - WLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYRK - LKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTAEVALGLVCATCEQIADSQHR - SHRQIATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAVEAMEVASQARQMVQAMRT - IGTHPSSSAGLRDDLLENLQAYQKRMGVQLQRFK" -ORIGIN - 1 gatgagtctt ctaaccgagg tcgaaacgta cgttctctct atcgtcccgt cgggccccct - 61 caaagccgag atcgcgcaga gacttgaaga tgtctttgca gggaagaaca ccgatcttga - 121 ggctctcatg gaatggctaa agacaagacc aatcctgtca cctctgacta aggggatttt - 181 ggggtttgtg ttcacgctca ccgtgcccag tgagcgagga ctgcagcgta gacgctttgt - 241 ccaaaatgct ctaaatggaa atggagaccc aaacaacatg gacagggcag tcaagctgta - 301 caggaaattg aagagagaga taacattcca tggggctaaa gaagttgcac tcagttactc - 361 aaccggtgca cttgccagtt gtatgggtct catatacaac aggatgggga cggtgaccgc - 421 agaagtggca ttgggcctag tgtgtgccac ctgtgagcag attgctgatt cacagcatcg - 481 gtctcacaga cagatagcta ccaccaccaa cccactaatc agacatgaaa acagaatggt - 541 gttggccagt actacagcta aggctatgga gcagatggct gggtcgagtg agcaagcagt - 601 ggaagccatg gaggttgcta gtcaggccag gcagatggtg caggcgatga ggaccattgg - 661 aactcatcct agctccagtg ccggtctgag agatgatctc cttgaaaatc tgcaggccta - 721 ccaaaaacgg atgggagtgc aactgcagcg attcaagtga tcctctcgtt attgccgcaa - 781 gtatcattgg gatcttgcac ttgatattgt ggattcttga tcgccttttc ttcaaatgcg - 841 tttatcgtcg ccttaaatac ggtttgaaaa gagggccttc tacggaagga gtacctgagt - 901 ccatgaggga agagtaccgg caggaacagc agagtgctgt ggatgttgac gatggtcatt - 961 ttgtcaacat agagctggag ta -// - diff --git a/config/reference_h5nx-2-year_na.gb b/config/reference_h5nx-2-year_na.gb deleted file mode 100644 index e25bd83..0000000 --- a/config/reference_h5nx-2-year_na.gb +++ /dev/null @@ -1,77 +0,0 @@ -LOCUS OL638147 1422 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 6 neuraminidase (NA) gene, complete cds. -ACCESSION OL638147 -VERSION OL638147.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 1422) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..1422 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="6" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 6..1415 - /gene="NA" - CDS 6..1415 - /gene="NA" - /codon_start=1 - /product="neuraminidase" - /protein_id="UFL16557.1" - /translation="MNPNQKITTIGSICMVIGIVSLMLQIGNIISIWVSHSIQTGNQY - QPEPCNQSIITYENNTWVNQTYVNISNTNFLAEQAVTSVTLAGNSSLCPISGWAIYSK - DNGIRIGSKGDVFVIREPFISCSHLXCRTFFLTQGALLNDKHSNGTVKDRSPYRTLMS - CPVGEAPSPYNSRFESVAWSASACHDGISWLTIGISGPDNGAVAVLKYNGIITDTIKS - WRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKIEKGKVVKSVELNAPNYHY - EECSCYPDAGDIMCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGS - CSPMSSNGAYGVKGFSFKYGNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVKQD - IVEITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGRPKENTIWTSGSSISFCGVNS - DTVGWSWPDGAELPFTIDK" -ORIGIN - 1 tcaaaatgaa tccaaatcaa aagataacaa ccattggatc aatctgtatg gtaattggga - 61 tagtcagctt gatgctgcaa attgggaata taatctcaat atgggttagc cattcaatcc - 121 aaacagggaa tcaataccag cctgaaccat gcaatcaaag catcattacc tatgagaaca - 181 acacctgggt aaatcagacg tatgtcaaca tcagcaatac caattttctt gctgagcagg - 241 ctgttacttc ggtaacatta gcgggcaatt catctctttg ccctattagt gggtgggcaa - 301 tatacagtaa ggacaacggt ataagaattg ggtccaaggg ggatgtgttt gttataagag - 361 aaccgttcat ctcatgctcc cacttggrat gcagaacctt tttcctgacc cagggagctc - 421 tgctgaatga caaacattct aatgggaccg ttaaggatag aagcccctat agaactttga - 481 tgagttgtcc cgtgggtgag gctccttccc cgtacaattc aagatttgag tctgttgctt - 541 ggtcggcaag tgcttgtcat gatggcatta gttggttgac aatcggtatt tctggtccag - 601 acaatggagc tgtggctgta ttgaagtaca atggcataat aacggatact atcaagagtt - 661 ggagaaacaa cattttgaga actcaagaat ctgaatgtgc gtgcgtaaat ggctcttgct - 721 tcactgtaat gactgatgga ccragcaatg ggcaggcctc atataaaatc ttcaagatag - 781 agaaagggaa agttgtcaaa tcagttgaat tgaatgcccc taattaccac tacgaggaat - 841 gctcctgtta tcctgatgcg ggtgatatta tgtgtgtgtg cagggacaat tggcatggct - 901 caaaccggcc gtgggtatct tttaatcaaa atctggagta tcaaatagga tatatatgca - 961 gtggggtttt cggggacaat ccccgcccca atgatggaac aggcagttgc agtccaatgt - 1021 cctctaacgg ggcatatggg gtaaaagggt tttcatttaa gtacggtaat ggggtttgga - 1081 tcggaagaac aaaaagcact agttccagaa gcggctttga gatgatttgg gatccgaatg - 1141 ggtggactga gacggacagt agtttctcag tgaagcaaga cattgtagaa ataactgact - 1201 ggtcaggata tagtggaagt tttgtccagc atccagaact gacaggatta gattgcatga - 1261 ggccttgttt ctgggttgag ctaattagag ggaggcccaa agagaacaca atttggacta - 1321 gcgggagcag catatccttt tgtggtgtaa atagtgacac tgtgggttgg tcttggccag - 1381 acggtgctga gttgccattc accattgaca agtagtttgt tc -// - diff --git a/config/reference_h5nx-2-year_np.gb b/config/reference_h5nx-2-year_np.gb deleted file mode 100644 index fb5dc94..0000000 --- a/config/reference_h5nx-2-year_np.gb +++ /dev/null @@ -1,79 +0,0 @@ -LOCUS OL638148 1513 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 5 nucleocapsid protein (NP) gene, partial cds. -ACCESSION OL638148 -VERSION OL638148.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 1513) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..1513 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="5" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 22..>1513 - /gene="NP" - CDS 22..>1513 - /gene="NP" - /codon_start=1 - /product="nucleocapsid protein" - /protein_id="UFL16558.1" - /translation="MASQGTKRSYEQMETGGERQNATEIRASVGRMVGGIGRFYIQMC - TELKLSDHEGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPVYRRRDG - KWVRELILYDKEEIRRIWRQANNGEDATAGLTHLMIWHSNLNDATYQRTRALVRAGMD - PRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIA - YERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCL - PACVYGLAVVSGYDFEREGYSLVGIDPFRLLQNSQVFSLIRPNENPAHKSQLVWMACH - SAAFEDLRVSSFIRGTRVVPRGQLSTRGVQIASNENMETMDSSTLELRSRYWAIRTRS - GGNTNQQRASAGQISVQPTFSVQRNLPFERATIMAAFTGNTEGRTSDMRTEIIRMMES - ARPEDVSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAEEYD" -ORIGIN - 1 tcactgagtg acatcaacat catggcgtct caaggcacca aacgatccta tgaacagatg - 61 gagactggtg gagagcgcca gaatgccact gagatcagag catctgttgg aagaatggtt - 121 ggtggaattg ggaggttcta catacagatg tgcactgagc tcaaactcag cgaccatgaa - 181 ggaaggctga tccagaacag cataacaata gagagaatgg ttctctctgc atttgatgaa - 241 aggaggaaca aatacctgga agaacacccc agtgcgggga aagacccgaa gaaaactgga - 301 ggtccagttt atcgaaggag agatgggaaa tgggtgagag aactgatcct gtatgacaaa - 361 gaggagatca ggagaatctg gcgtcaagcg aacaatggag aagacgcaac tgctggtctc - 421 actcacctga tgatctggca ttctaatcta aatgatgcca cataccagag gacaagagct - 481 ctcgtgcgtg ctgggatgga ccccaggatg tgctctctta tgcaaggatc aactctccca - 541 aggaggtctg gagctgctgg tgcagcagta aagggagtcg ggacgatggt gatggaacta - 601 attcggatga taaagcgagg aattaatgat cggaacttct ggagaggcga gaacggacga - 661 aggacaagga ttgcatatga gagaatgtgc aacatcctca aagggaaatt ccaaacagca - 721 gcgcaaagag caatgatgga ccaggtgcgt gaaagcagga atcctggcaa tgctgaaatt - 781 gaagatctca tctttctggc acggtctgca ctcatcctga gaggatcagt ggctcataag - 841 tcctgcttgc ctgcttgtgt gtacggactc gctgtggtca gtggatacga ctttgagaga - 901 gaagggtact ctctagttgg aatagatcct ttccgtctgc ttcaaaacag ccaggtcttc - 961 agcctcatta gaccaaatga gaatccagca cacaagagtc aattggtatg gatggcatgt - 1021 cattcagcag cattcgagga tctgagagtc tcaagtttca tcagaggaac aagagtagtt - 1081 ccaagaggac aactatccac aagaggggtt caaattgctt caaatgaaaa catggaaaca - 1141 atggactcca gcactcttga actgagaagc agatattggg ctataagaac caggagtgga - 1201 ggaaacacca accaacagag agcatctgca ggacagatca gtgtacagcc cactttttcg - 1261 gtacagagaa atcttccctt tgaaagagcg accattatgg cggcgttcac agggaatact - 1321 gagggcagaa catccgacat gaggactgaa atcataagaa tgatggaaag tgccagacca - 1381 gaagatgtgt ctttccaggg gcggggagtc ttcgagcttt cggacgaaaa ggcaacgaac - 1441 ccgatcgtgc cttcctttga catgagtaat gaaggatctt atttcttcgg agacaatgca - 1501 gaggagtatg aca -// - diff --git a/config/reference_h5nx-2-year_ns.gb b/config/reference_h5nx-2-year_ns.gb deleted file mode 100644 index 79d9f72..0000000 --- a/config/reference_h5nx-2-year_ns.gb +++ /dev/null @@ -1,78 +0,0 @@ -LOCUS OL638149 850 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 8 nuclear export protein (NEP) and nonstructural protein 1 - (NS1) genes, complete cds. -ACCESSION OL638149 -VERSION OL638149.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 850) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..850 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="8" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 7..844 - /gene="NEP" - /gene_synonym="NS2" - CDS join(7..36,509..844) - /gene="NEP" - /gene_synonym="NS2" - /note="nonstructural protein 2" - /codon_start=1 - /product="nuclear export protein" - /protein_id="UFL16560.1" - /translation="MDSNTVSSFQDILMRMSKMQLGSSSEDLNGMITQFGSLKLYRDS - LGEAVMRMGDLHSLQSRNGKWREQLSQKFEEIRWLIEEVRHRLKITENSFEQITFMQA - LQLLLEVEQEIRTFSFQLI" - gene 7..699 - /gene="NS1" - CDS 7..699 - /gene="NS1" - /codon_start=1 - /product="nonstructural protein 1" - /protein_id="UFL16559.1" - /translation="MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLR - GRGSTLGLDIETATRAGKQIVERILEEESDEALKMTIAPVPASRYLTDMTLEEMSRDW - FMLMPKQKVAGSLCIRMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEI - SPLPSLPGHTDEDVKNAIGVLIGGLEWNDNTVRVSETLQRFAWGSSNEDGRPPLPPKQ - KRKMARTIESEV" -ORIGIN - 1 aacataatgg attccaacac tgtgtcaagc tttcaggtag actgctttct ttggcatgtc - 61 cgcaaacgat ttgcagacca agaactgggt gatgccccat tccttgaccg gcttcgccga - 121 gatcagaaat ccctgagagg aagaggcagc actcttggtc tggacatcga aacagccacc - 181 cgtgcgggaa agcagatagt ggagcggatt ctggaagaag agtctgatga ggcacttaaa - 241 atgactattg cccccgtgcc agcttcacgc tacctaactg acatgactct tgaggagatg - 301 tcaagggact ggttcatgct catgcccaaa cagaaagtgg caggttccct ttgcatcaga - 361 atggaccagg caataatgga taaaaccatc atattgaaag caaacttcag tgtgattttt - 421 gaccggctgg aaaccctaat actacttaga gctttcacag aagaaggagc aattgtggga - 481 gaaatctcac cattaccttc tcttccagga catactgatg aggatgtcaa aaatgcaatt - 541 ggggtcctca tcggaggact tgaatggaat gataacacag ttcgggtctc tgaaactcta - 601 cagagattcg cttggggaag cagtaatgag gatgggagac ctccactccc tccaaagcag - 661 aaacggaaaa tggcgagaac aattgagtca gaagtttgaa gaaataagat ggctgattga - 721 agaagtgcgg cacagattga agattacaga gaacagtttc gaacagataa cttttatgca - 781 agccttacaa ctattgcttg aagtggagca agagataaga actttctcgt ttcagcttat - 841 ttaatgataa -// - diff --git a/config/reference_h5nx-2-year_pa.gb b/config/reference_h5nx-2-year_pa.gb deleted file mode 100644 index 207a773..0000000 --- a/config/reference_h5nx-2-year_pa.gb +++ /dev/null @@ -1,108 +0,0 @@ -LOCUS OL638150 2190 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, - complete cds. -ACCESSION OL638150 -VERSION OL638150.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 2190) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..2190 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="3" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 1..2151 - /gene="PA" - CDS 1..2151 - /gene="PA" - /codon_start=1 - /product="polymerase PA" - /protein_id="UFL16561.1" - /translation="MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEV - CFMYSDFHFIDERGESMIVEPGDPNALLKHRFEIIEGRDRAMAWTVVNSICNTTGVEK - PKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKAD - YTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQS - LPPSFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVKARIEPFMKTTPRPLRLPDGPPC - SQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNY - LLAWKQVLAELQDIENEEKFPKTKNMKKTSQLKWALGENMAPEKVDFEDCKDVSDLRQ - YDSDEPESRSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV - SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGR - SHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVR - TNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMSKEFFENKSETWPIGES - PKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFD - LGGLYEAIEECLINDPWVLLNASWFNSFLTHALK" - gene 1..760 - /gene="PA-X" - CDS join(1..570,572..760) - /gene="PA-X" - /ribosomal_slippage - /codon_start=1 - /product="PA-X protein" - /protein_id="UFL16562.1" - /translation="MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEV - CFMYSDFHFIDERGESMIVEPGDPNALLKHRFEIIEGRDRAMAWTVVNSICNTTGVEK - PKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKAD - YTLDEESRARIKTRLFTIRQEMASRGLWDSFVSPREAKRQLKKDLKSQEPCAGLPTKV - SHRASPALKTLEPMWMDSNRTAALRASFLKCQKK" -ORIGIN - 1 atggaagact ttgtgcgaca atgcttcaat ccaatgattg tcgagcttgc ggaaaaagca - 61 atgaaagaat atggggaaga tccgaaaatc gagacaaaca aatttgccgc aatatgcaca - 121 cacttagaag tctgtttcat gtattcagat ttccatttta tcgatgaacg aggcgaatca - 181 atgattgtag aacctggcga tccaaatgca ttattgaaac accgatttga gataatcgaa - 241 gggagagacc gagcaatggc ctggacagtg gtgaatagta tctgcaacac cacaggggtc - 301 gaaaagccca aattcctccc tgatttgtat gactacaaag agaatcgatt cattgaaatt - 361 ggagtaacgc gaagggaagt tcacatatac tatttagaaa aagccaacaa gataaagtca - 421 gagaaaacac acattcacat attctcattc actggagagg aaatggccac caaggcggac - 481 tacacccttg atgaagagag cagagcaaga ataaaaacca gactgttcac tataagacaa - 541 gaaatggcca gtagaggtct atgggattcc tttcgtcagt ccgagagagg cgaagagaca - 601 attgaagaaa gatttgaaat cacaggaacc atgcgcaggc ttgccgacca aagtctccca - 661 ccgagcttct ccagccttga aaactttaga gcctatgtgg atggattcga accgaacggc - 721 tgcattgagg gcaagctttc tcaaatgtca aaagaagtga aagccagaat tgagccattt - 781 atgaagacaa caccacgccc tctcagatta cctgatgggc ctccctgttc tcagcggtcg - 841 aagttcttgc tgatggatgc ccttaagttg agcatcgaag accctagcca tgagggggag - 901 ggcataccgc tgtatgatgc aatcaaatgc atgaagacat tttttggctg gaaagagccc - 961 aacatcgtaa agccgcatga gaaaggcata aaccctaatt acctcctggc ttggaagcag - 1021 gtgctggcag aacttcaaga cattgaaaat gaggagaaat ttccaaaaac aaagaacatg - 1081 aagaaaacaa gccaattgaa gtgggcactt ggtgagaaca tggctccaga aaaagtggac - 1141 tttgaggact gcaaagatgt tagcgatcta agacagtacg acagtgacga accagagtct - 1201 agatcactag caagctggat tcagagtgaa ttcaacaagg catgcgaact gacagattcg - 1261 agttggattg aacttgatga gataggggaa gacgttgctc caatcgaaca cattgcgagt - 1321 atgaggagga actatttcac agcggaggta tcccattgca gggccactga atacataatg - 1381 aagggagtat acataaatac agccctattg aatgcatcct gtgcagccat ggatgacttc - 1441 caactgattc caatgataag caagtgcaga actaaagaag gaagacggaa gacaaatctg - 1501 tatggattca ttataaaagg aagatcccat ttgaggaatg acaccgatgt ggtaaacttt - 1561 gtgagcatgg aattctctct aactgacccg aggctagagc cacacaaatg ggaaaagtac - 1621 tgtgttcttg agataggaga catgctccta cggactgcaa taggccaagt gtcgaggccc - 1681 atgttcctgt atgtgagaac caatgggact tccaagatca aaatgaaatg gggcatggag - 1741 atgagacgat gccttcttca gtcccttcaa caaattgaga gcatgattga ggccgaatct - 1801 tctgtcaaag agaaggacat gtccaaggaa ttctttgaaa acaaatcaga aacatggcca - 1861 attggagaat cacccaaagg ggtggaggaa ggctctattg ggaaagtatg cagaacattg - 1921 ctagcaaagt ctgtgttcaa cagcctatat gcatctccac aactcgaggg gttttcagct - 1981 gaatcaagaa aattgcttct cattgttcag gcacttaggg acaacctgga acctggaacc - 2041 ttcgatcttg gggggctata tgaagcaatt gaggagtgcc tgattaacga tccctgggtt - 2101 ttgcttaatg cgtcttggtt caactccttc ctcacacatg cactgaaata gttgtggcaa - 2161 tgctactatt tgctatccat actgtccaaa -// - diff --git a/config/reference_h5nx-2-year_pb1.gb b/config/reference_h5nx-2-year_pb1.gb deleted file mode 100644 index 4f55fb4..0000000 --- a/config/reference_h5nx-2-year_pb1.gb +++ /dev/null @@ -1,107 +0,0 @@ -LOCUS OL638151 2299 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) genes, - complete cds. -ACCESSION OL638151 -VERSION OL638151.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 2299) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..2299 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="2" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 1..2274 - /gene="PB1" - CDS 1..2274 - /gene="PB1" - /codon_start=1 - /product="polymerase PB1" - /protein_id="UFL16563.1" - /translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN - RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI - FGNSCIETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES - GRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNRRSYL - IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN - EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR - NVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEILANIDLKYFNESTRKKIEKI - RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALI - VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSME - LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT - QIQTRRSFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRL - CNPLNPFVSHKEIESVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI - LEDEQMYQKCCSLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKGEF - AEIMKICSTIEELRRQK" - gene 95..367 - /gene="PB1-F2" - CDS 95..367 - /gene="PB1-F2" - /codon_start=1 - /product="PB1-F2 protein" - /protein_id="UFL16564.1" - /translation="MEQGQDTQWTQSTEHINTQRRENGQQTQKPEHLNSTQLMGHYLR - TTNRADMHRQIACWKQWLSLKSPTQGSLETLVLKRWKSFSKQEWTN" -ORIGIN - 1 atggatgtca atccgacttt acttttctta aaagtgccag cgcaaaatgc cataagtacc - 61 acattccctt atactggaga tcctccatac agccatggaa cagggacagg atacacaatg - 121 gacacagtca acagaacaca tcaatactca gagaagggaa aatggacaac aaacacagaa - 181 accggagcac ctcaactcaa cccaattgat gggccactac ctgaggacaa cgaaccgagc - 241 ggatatgcac agacagattg cgtgttggaa gcaatggctt tccttgaaga gtcccaccca - 301 gggatctttg gaaactcttg tattgaaacg atggaagtcg ttcagcaaac aagagtggac - 361 aaactaactc aaggtcgcca gacttatgac tggacactga atagaaacca accagctgca - 421 actgccctgg ccaacactat agaggtcttc agatcaaacg gtctaacagc caatgaatcg - 481 gggagactaa tagatttcct caaggatgtg atggactcaa tggataaaga agaaatggaa - 541 ataacaacac atttccagag aaagagaaga gtaagggaca acatgaccaa gaaaatggtc - 601 acacaaagaa caataggaaa gaagaaacaa aggctaaaca ggaggagcta cttaataaga - 661 gcactgacac tgaatacaat gacaaaagat gcagaaagag gcaaattgaa gagacgggcg - 721 attgcaacac cagggatgca gattagagga tttgtgtact ttgtcgaaac actggcaagg - 781 agcatctgtg aaaaacttga gcaatctgga ctccccgttg gaggaaatga gaagaaggct - 841 aaattggcaa atgtcgtgag gaaaatgatg actaactcac aagatacaga gctctccttc - 901 acaattactg gagataacac caaatggaat gagaatcaaa atcctcggat gtttctggca - 961 atgataacgt acattacaag aaaccaacct gaatggttta gaaatgtctt gagtattgcc - 1021 cctataatgt tctcgaacaa aatggcgaga ttgggaaaag ggtacatgtt tgaaagtaag - 1081 agcatgaagt tacggacaca aatacctgca gaaatacttg caaacattga cttaaaatac - 1141 ttcaatgaat caacaagaaa gaaaatcgaa aaaataaggc ctctactaat agatggcact - 1201 gcctcattga gtcctggaat gatgatgggc atgttcaata tgctgagtac agtattagga - 1261 gtttcaatcc taaatcttgg gcaaaagagg tacaccaaaa ccacatactg gtgggatgga - 1321 ctccaatcct ctgatgattt cgccctcata gtaaatgcac cgaatcatga gggaatacaa - 1381 gcaggagtgg ataggttcta taggacctgc aaactggtcg gaatcaatat gagcaaaaag - 1441 aagtcttaca taaaccggac tggaacattt gagttcacaa gctttttcta tcgctatgga - 1501 tttgtggcta acttcagtat ggagctgccc agctttggag tttctggaat caatgaatca - 1561 gctgacatga gcattggcgt cacagtgata aagaacaaca tgataaacaa tgaccttgga - 1621 ccagcaacag ctcaaatggc ccttcaacta ttcatcaaag attacaggta cacgtaccga - 1681 tgccacagag gtgacacaca aattcaaacg aggagatcat tcgagctgaa gaagctgtgg - 1741 gaacagaccc gttcaaaggc aggactgttg gtgtcagatg gaggaccaaa tctatacaac - 1801 attcggaatc tccatatccc agaggtctgc ctgaagtggg agctgatgga cgaagattac - 1861 cagggcaggt tgtgtaatcc tctgaaccca tttgtcagtc ataaagaaat tgagtccgta - 1921 aacaatgccg tggtgatgcc agcccacggt ccagccaaaa gcatggaata tgatgccgtt - 1981 gcgactacac actcatggat tcctaaaagg aatcgttcca ttctcaatac cagccaaagg - 2041 ggaattcttg aggatgaaca gatgtaccag aaatgctgca gtctattcga gaaattcttc - 2101 cccagtagtt catacaggag accagttgga atttccagca tggtggaggc catggtgtct - 2161 agggcccgaa tcgatgcacg cattgatttc gaatctggaa ggatcaagaa gggagagttt - 2221 gctgagatca tgaagatctg ttccaccatt gaagagctca gacggcaaaa atagtgaatt - 2281 tagcttgtcc ttcatgaaa -// - diff --git a/config/reference_h5nx-2-year_pb2.gb b/config/reference_h5nx-2-year_pb2.gb deleted file mode 100644 index b0c224e..0000000 --- a/config/reference_h5nx-2-year_pb2.gb +++ /dev/null @@ -1,97 +0,0 @@ -LOCUS OL638152 2298 bp cRNA linear VRL 01-DEC-2021 -DEFINITION Influenza A virus (A/goose/Czech Republic/18520-2/2021(H5N1)) - segment 1 polymerase PB2 (PB2) gene, complete cds. -ACCESSION OL638152 -VERSION OL638152.1 -KEYWORDS . -SOURCE Influenza A virus - ORGANISM Influenza A virus - Viruses; Riboviria; Orthornavirae; Negarnaviricota; - Polyploviricotina; Insthoviricetes; Articulavirales; - Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus - influenzae. -REFERENCE 1 (bases 1 to 2298) - AUTHORS Nagy,A., Cernikova,L. and Stara,M. - TITLE Direct Submission - JOURNAL Submitted (26-NOV-2021) Molecular Biology, State Veterinary - Institute Prague, Sidlistni 136/24, Prague 16503, Czech Republic -COMMENT ##Assembly-Data-START## - Assembly Method :: Samtools, BCFtools v. 2021 - Sequencing Technology :: ONT - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..2298 - /organism="Influenza A virus" - /mol_type="viral cRNA" - /strain="A/goose/Czech Republic/18520-2/2021" - /serotype="H5N1" - /isolate="18520-2" - /isolation_source="organs" - /host="goose" - /db_xref="taxon:11320" - /segment="1" - /country="Czech Republic" - /collection_date="27-Sep-2021" - gene 4..2283 - /gene="PB2" - CDS 4..2283 - /gene="PB2" - /codon_start=1 - /product="polymerase PB2" - /protein_id="UFL16565.1" - /translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA - LRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN - GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHSDLSAKEAQ - DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL - PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADP - LASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS - GSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQ - SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG - VEPIDSVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQR - GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQ - DPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA - PPEQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEG - TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD - SSILTDSQTATKRIRMAIN" -ORIGIN - 1 aatatggaaa gaataaaaga gctaagagat ttgatgtcgc agtctcgcac tcgcgagata - 61 ctaacaaaaa ccactgtgga ccatatggcc ataatcaaga aatatacatc aggaagacag - 121 gagaagaacc ctgcacttag gatgaaatgg atgatggcaa tgaaatatcc gattacagcg - 181 gacaaaagga taatggagat gatccctgaa agaaatgagc aaggtcagac cctttggagc - 241 aaaacaaatg atgctggatc agacagagtg atggtgtcac ctctggctgt gacgtggtgg - 301 aataggaatg gaccaacaac aagtacagtc cattacccaa aggtctataa aacttacttt - 361 gaaaaggttg aaaggttaaa acatggaacc ttcggccctg ttcattttcg aaatcaagtc - 421 aagatacgcc gcagagttga cataaacccg ggccattcag accttagtgc taaagaagca - 481 caagacgtca tcatggaggt cgttttccca aatgaagtcg gagccagaat attaacatca - 541 gagtcacagt taacaataac aaaagaaaag aaggaggaac tccaggactg taagattgcc - 601 ccyttaatgg tggcatacat gttggagaga gagctggttc gaaaaaccag attcctgcca - 661 gtagctggcg gaacaagcag cgtatatatc gaggtattgc acttgactca aggaacctgc - 721 tgggaacaaa tgtatacgcc aggaggagaa gtgagaaatg atgatgttga tcagagttta - 781 attattgctg ccagaaatat cgttaggaga gcaacagtat cagcagaccc attggcttcg - 841 ctactggaga tgtgccatag tacacaaatt ggcgggataa ggatggtaga cattcttaga - 901 cagaacccaa cagaagagca agctgtggat atatgcaaag cagcaatggg tctaagaatc - 961 agttcatcct tcagctttgg tggtttcact ttcaaaagga caagtggatc atctgtcaaa - 1021 agagaagagg aagtgctcac cggcaacctc caaacattga aaataagagt gcatgaaggg - 1081 tatgaggaat tcacaatggt tggacgaaga gcaacagcca ttctaaggaa agcaaccaga - 1141 aggctgatcc aattgatagt gagtggaaga gacgagcagt caatcgccga agcgatcata - 1201 gttgcaatgg tgttctccca agaggattgc atgataaagg cagtacgagg tgatttaaat - 1261 tttgtcaata gagcaaatca gcggctaaat cctatgcatc agctcctgag gcatttccaa - 1321 aaagatgcaa aggtactgtt ccaaaactgg ggggttgaac ccattgacag tgtcatgggg - 1381 atgataggaa tattgcctga tatgacaccc agcacagaga tgtcactaag aggagtgagr - 1441 gtcagtaaaa tgggagtgga tgaatattcc agtactgaga gggtggtcgt gagtattgat - 1501 cgcttcttaa gggtccgaga ccagagagga aacgtacttt tgtctcctga agaggttagt - 1561 gaaacacagg gaacagagaa gctgacgata acatattcat catccatgat gtgggaaatt - 1621 aatggtccgg aatcagtgtt ggttaacaca tatcaatgga tcatcaggaa ctgggaaacc - 1681 gtgaagattc agtggtccca agaccctaca atgctataca acaagatgga gtttgagccc - 1741 tttcagtcct tggtgcctaa ggcggccaga ggccagtaca gtggatttgt aaggactcta - 1801 ttccagcaga tgcgtgatgt gctggggacc tttgacactg tccagataat aaagctactc - 1861 ccatttgcag cagccccacc ggaacaaagt aggatgcaat tctcttcttt aactgtaaac - 1921 gtacggggtt caggaatgag gatacttgtg agaggcaact cccctgtgtt caactataac - 1981 aaggcaacca agaggctcac agtccttgga aaggatgctg gtgcattgac agaagacccg - 2041 gatgagggaa cggcaggagt ggagtccgcg gtattgagag ggttcctaat tctgggcaaa - 2101 gaagacaaaa ggtatggacc agcgctgagc atcaatgaat tgagcaatct tgctaaaggg - 2161 gagaaggcta atgtgttgat agggcaagga gacgtggtgt tggtgatgaa acggaaacgg - 2221 gactctagca tacttactga cagccagaca gcgaccaaaa gaattcggat ggccatcaat - 2281 tagtgtcgaa ttgtttaa -// - diff --git a/config/reference_h5nx-all-time_ha.gb b/config/reference_h5nx-all-time_ha.gb deleted file mode 100755 index a3fa17c..0000000 --- a/config/reference_h5nx-all-time_ha.gb +++ /dev/null @@ -1,87 +0,0 @@ -LOCUS AF144305 1760 bp cRNA linear VRL 10-JUL-2007 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) hemagglutinin (HA) - gene, complete cds. -ACCESSION AF144305 -VERSION AF144305.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 1760) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 1760) - CONSRTM World Health Organization Global Influenza Program Surveillance - Network - TITLE Evolution of H5N1 avian influenza viruses in Asia - JOURNAL Emerging Infect. Dis. 11 (10), 1515-1521 (2005) - PUBMED 16318689 -REFERENCE 3 (bases 1 to 1760) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..1760 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="viral cRNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 22..1728 - /gene="HA" - CDS 22..1728 - /gene="HA" - /codon_start=1 - /product="hemagglutinin" - /protein_id="AAD51927.1" - /translation="MEKIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTH - AQDILEKTHNGKLCDLNGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKASPA - NDLCYPGDFNDYEELKHLLSRTNHFEKIQIIPKSSWSNHDASSGVSSACPYHGRSSFF - RNVVWLIKKNSAYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGT - STLNQRLVPEIATRPKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKG - DSAIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLR - NTPQRERRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAID - GVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKQMEDGFLDVWTYNAELLVLMEN - ERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVKNGTYDYPQY - SEEARLNREEISGVKLESMGTYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCRI - CI" -ORIGIN - 1 gcaggggtat aatctgtcaa aatggagaaa atagtgcttc ttcttgcaat agtcagtctt - 61 gtcaaaagtg atcagatttg cattggttac catgcaaaca actcgacaga gcaggttgac - 121 acaataatgg aaaagaacgt tactgttaca catgcccaag acatactgga aaagacacac - 181 aatgggaagc tctgcgatct aaatggagtg aagcctctca ttttgagaga ttgtagtgta - 241 gctggatggc tcctcggaaa ccctatgtgt gacgaattca tcaatgtgcc ggaatggtct - 301 tacatagtgg agaaggccag tccagccaat gacctctgtt acccagggga tttcaacgac - 361 tatgaagaac tgaaacacct attgagcaga acaaaccatt ttgagaaaat tcagatcatc - 421 cccaaaagtt cttggtccaa tcatgatgcc tcatcagggg tgagctcagc atgtccatac - 481 catgggaggt cctccttttt cagaaatgtg gtatggctta tcaaaaagaa cagtgcatac - 541 ccaacaataa agaggagcta caataatacc aaccaagaag atcttttagt actgtggggg - 601 attcaccatc ctaatgatgc ggcagagcag acaaagctct atcaaaaccc aaccacttac - 661 atttccgttg gaacatcaac actgaaccag agattggttc cagaaatagc tactagaccc - 721 aaagtaaacg ggcaaagtgg aagaatggag ttcttctgga caattttaaa gccgaatgat - 781 gccatcaatt tcgagagtaa tggaaatttc attgctccag aatatgcata caaaattgtc - 841 aagaaagggg actcagcaat tatgaaaagt gaattggaat atggtaactg caacaccaag - 901 tgtcaaactc caatgggggc gataaactct agtatgccat tccacaacat acaccccctc - 961 accatcgggg aatgccccaa atatgtgaaa tcaaacagat tagtccttgc gactggactc - 1021 agaaataccc ctcagagaga gagaagaaga aaaaagagag gactatttgg agctatagca - 1081 ggttttatag agggaggatg gcagggaatg gtagatggtt ggtatgggta ccaccatagc - 1141 aatgagcagg ggagtggata cgctgcagac aaagaatcca ctcaaaaggc aatagatgga - 1201 gtcaccaata aggtcaactc gatcattgac aaaatgaaca ctcagtttga ggccgttgga - 1261 agggaattta ataacttgga aaggaggata gagaatttaa acaagcagat ggaagacgga - 1321 ttcctagatg tctggactta taatgctgaa cttctggttc tcatggaaaa tgagagaact - 1381 ctagactttc atgactcaaa tgtcaagaac ctttatgaca aggtccgact acagcttagg - 1441 gataatgcaa aggagctggg taatggttgt ttcgagttct atcacaaatg tgataatgaa - 1501 tgtatggaaa gtgtaaaaaa cggaacgtat gactacccgc agtattcaga agaagcaaga - 1561 ctaaacagag aggaaataag tggagtaaaa ttggaatcaa tgggaactta ccaaatactg - 1621 tcaatttatt caacagtggc gagttcccta gcactggcaa tcatggtagc tggtctatct - 1681 ttatggatgt gctccaatgg atcgttacaa tgcagaattt gcatttaaat ttgtgagttc - 1741 agattgtagt taaaaacacc -// - diff --git a/config/reference_h5nx-all-time_mp.gb b/config/reference_h5nx-all-time_mp.gb deleted file mode 100755 index 079e9e1..0000000 --- a/config/reference_h5nx-all-time_mp.gb +++ /dev/null @@ -1,78 +0,0 @@ -LOCUS AF144306 1027 bp cRNA linear VRL 10-JUL-2007 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) matrix proteins M1 - and M2 (M) gene, alternatively spliced products, complete cds. -ACCESSION AF144306 -VERSION AF144306.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 1027) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 1027) - CONSRTM World Health Organization Global Influenza Program Surveillance - Network - TITLE Evolution of H5N1 avian influenza viruses in Asia - JOURNAL Emerging Infect. Dis. 11 (10), 1515-1521 (2005) - PUBMED 16318689 -REFERENCE 3 (bases 1 to 1027) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..1027 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="viral cRNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 26..1007 - /gene="M" - CDS join(26..51,740..1007) - /gene="M2" - /note="M2" - /codon_start=1 - /product="matrix protein 2" - /protein_id="AAD51929.1" - /translation="MSLLTEVETPTKNEWECKCSDSSDPLVVAASIIGILHLILWILD - RLFFKCIYRRLKYGLKRGPSTEGVPESMREEYRQEQQSAVDVDDGHFVNIELE" - CDS 26..784 - /gene="M1" - /note="M1" - /codon_start=1 - /product="matrix protein 1" - /protein_id="AAD51928.1" - /translation="MSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEALME - WLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYKK - LKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQHR - SHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVASQARQMVQAMRT - IGTHPSSSAGLKDNLLENLQAYQKRMGVQMQRFK" -ORIGIN - 1 agcaaaagca ggtagatatt gaaaaatgag tcttctaacc gaggtcgaaa cgtacgttct - 61 ctctatcgtc ccgtcaggcc ccctcaaagc cgagatcgcg cagagacttg aggatgtctt - 121 tgcaggaaag aacaccgatc tcgaggctct catggaatgg ctaaagacaa gaccaatcct - 181 gtcacctctg actaaaggga ttttaggatt tgtgttcacg ctcaccgtgc ccagtgagcg - 241 aggactgcag cgtagacgct ttgtccagaa tgccttaaat ggaaatggag atccaaacaa - 301 tatggatagg gcagttaagc tatacaagaa gctgaaaaga gaaataacat tccatggggc - 361 taaggaggtc gcactcagct actcaaccgg tgcacttgcc agttgtatgg gtctcatata - 421 caacaggatg ggaacggtga ccacagaagt ggcttttggc ctagtgtgtg ccacttgtga - 481 gcagattgca gattcacagc atcggtctca cagacagatg gcaactacca ccaacccact - 541 aatcaggcat gagaacagaa tggtgctggc cagcactaca gctaaggcta tggagcagat - 601 ggctggatcg agtgagcagg cagcggaagc catggaggtt gctagtcagg ctaggcagat - 661 ggtgcaggca atgaggacaa ttgggactca tcctagctcc agtgccggtc tgaaagataa - 721 tcttcttgaa aatttgcagg cctaccaaaa acgaatggga gtgcaaatgc agcgattcaa - 781 gtgatcctct tgttgttgcc gcaagtatca ttgggatact gcacttgata ttgtggattc - 841 ttgatcgtct tttcttcaaa tgcatttatc gtcgccttaa atacggtttg aaaagagggc - 901 cttctacgga aggggtacct gagtctatga gggaagagta tcggcaggaa cagcagagtg - 961 ctgtggatgt tgacgatggt cattttgtca acatagagct ggagtaaaaa actaccttgt - 1021 ttctact -// - diff --git a/config/reference_h5nx-all-time_na.gb b/config/reference_h5nx-all-time_na.gb deleted file mode 100755 index 0aa3e54..0000000 --- a/config/reference_h5nx-all-time_na.gb +++ /dev/null @@ -1,80 +0,0 @@ -LOCUS AF144304 1458 bp cRNA linear VRL 10-JUL-2007 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) neuraminidase (NA) - gene, complete cds. -ACCESSION AF144304 -VERSION AF144304.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 1458) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 1458) - CONSRTM World Health Organization Global Influenza Program Surveillance - Network - TITLE Evolution of H5N1 avian influenza viruses in Asia - JOURNAL Emerging Infect. Dis. 11 (10), 1515-1521 (2005) - PUBMED 16318689 -REFERENCE 3 (bases 1 to 1458) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..1458 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="viral cRNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 21..1430 - /gene="NA" - CDS 21..1430 - /gene="NA" - /codon_start=1 - /product="neuraminidase" - /protein_id="AAD51926.1" - /translation="MNPNQKIITIGSICMVVGIISLMLQIGNIISIWVSHSIQTGNQH - QAEPCNQSIITYENNTWVNQTYVNISNTNFLTEKAVASVTLAGNSSLCPISGWAVHSK - DNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPHRTLMS - CPVGEAPSPYNSRFESVAWSASACHDGTSWLTIGISGPDNGAVAVLKYNGIITDTIKS - WRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFKMEKGKVVKSVELNAPNYHY - EECSCYPDAGEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGVFGDNPRPNDGTGS - CGPVSPNGAYGVKGFSFKYGNGVWIGRTKSTNSRSGFEMIWDPNGWTGTDSSFSVKQD - IVAITDWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKESTIWTSGSSISFCGVNS - DTVGWSWPDDAELPFTIDK" -ORIGIN - 1 agcaaaagca ggagattaaa atgaatccaa atcagaagat aataaccatt ggatcaatct - 61 gtatggtagt tgggataatt agcttgatgt tacaaattgg gaacataatc tcaatatggg - 121 tcagtcattc aattcagaca gggaatcaac accaagctga accatgcaat caaagcatta - 181 ttacttatga aaacaacacc tgggtaaatc aaacatatgt caacatcagc aataccaatt - 241 ttcttactga aaaagctgtg gcttcagtaa cattagcggg caattcatct ctttgcccca - 301 ttagcggatg ggctgtacac agtaaggaca acggtataag aatcggttcc aagggggatg - 361 tgtttgttat aagagagccg ttcatctcat gctcccactt ggaatgcaga actttctttt - 421 tgactcaggg agccttgctg aatgacaagc actccaatgg gaccgtcaaa gacagaagcc - 481 ctcacagaac attgatgagt tgtcctgtgg gtgaggctcc ctccccatat aactcaaggt - 541 ttgagtctgt tgcttggtcg gcaagtgctt gccatgatgg caccagttgg ttgacaattg - 601 gaatttctgg cccagacaat ggggctgtgg ctgtattgaa atacaacggc ataataacag - 661 acactatcaa gagttggagg aacaacatac tgagaactca agagtctgaa tgtgcatgtg - 721 taaatggctc ttgctttact gtaatgactg acggaccaag taatgggcag gcctcatata - 781 agatcttcaa aatggaaaaa gggaaagtag ttaaatcagt cgaattgaat gcccctaatt - 841 atcactatga ggagtgctcc tgttatcctg atgctggcga aatcacatgt gtgtgcaggg - 901 ataattggca tggctcaaat cggccatggg tatctttcaa tcaaaatttg gagtatcaaa - 961 taggatatat atgcagtgga gttttcggag acaatccacg ccccaatgat ggaacaggca - 1021 gttgtggtcc ggtgtcccct aacggggcat atggagtaaa agggttttca tttaaatacg - 1081 gcaatggtgt ttggatcggg agaaccaaaa gcactaattc caggagcggc tttgaaatga - 1141 tttgggatcc aaatgggtgg actggaacgg acagtagctt ctcggtgaaa caagatatcg - 1201 tagcaataac tgattggtca ggatatagcg ggagttttgt ccagcatcca gaactgacag - 1261 gattagattg cataagacct tgtttctggg ttgagctaat cagagggcgg cccaaagaga - 1321 gcacaatttg gactagtggg agcagcatat ctttttgtgg tgtaaatagt gacactgtgg - 1381 gttggtcttg gccagacgat gccgagttgc cattcaccat tgacaagtag tttgttcaaa - 1441 aaactccttg tttctact -// - diff --git a/config/reference_h5nx-all-time_np.gb b/config/reference_h5nx-all-time_np.gb deleted file mode 100755 index 17474fa..0000000 --- a/config/reference_h5nx-all-time_np.gb +++ /dev/null @@ -1,76 +0,0 @@ -LOCUS AF144303 1565 bp RNA linear VRL 31-AUG-1999 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) nucleocapsid - protein (NP) gene, complete cds. -ACCESSION AF144303 -VERSION AF144303.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 1565) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 1565) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..1565 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="genomic RNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 46..1542 - /gene="NP" - CDS 46..1542 - /gene="NP" - /codon_start=1 - /product="nucleocapsid protein" - /protein_id="AAD51925.1" - /translation="MASQGTKRSYEQMETGGERQNATEIRASVGRMVGGIGRFYIQMC - TELKLSDYEGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRRDG - KWVRELILYDKEEIRRIWRQANNGEDATAGLTHMMIWHSNLNDATYQRTRALVRTGMD - PRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIA - YERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCL - PACVYGLAVASGYDFEREGYSLVGIDPFRLLQNSQVFSLIRPNENPAHKSQLVWMACH - SAAFEDLRVSSFIRGTRVAPRGQLSTRGVQIASNENMETMDSSTLELRSRYWAIRTRS - GGNTNQQRASAGQISVQPTFSVQRNLPFERATIMAAFTGNTEGRTSDMRTEIIRMMES - SRPEDVSFQGRGVFELSDEKATNPIVPSFDMSNEGSYFFGDNAEEYDN" -ORIGIN - 1 agcaaaagca gggtagataa tcactcactg agtgacatca acatcatggc gtctcagggc - 61 accaaacgat cttatgaaca gatggaaact ggtggagaac gccagaatgc tactgagatc - 121 agagcatctg ttggaagaat ggttggtgga attgggaggt tttatataca gatgtgcact - 181 gaactcaaac tcagcgacta tgaaggaagg ctgattcaga acagcataac aatagagaga - 241 atggttctct ctgcatttga tgaaaggagg aacaaatacc tggaagaaca tcccagtgcg - 301 gggaaggacc caaagaaaac tggaggtcca atctaccgaa gaagagacgg aaaatgggtg - 361 agagagctga ttctgtatga caaagaggag atcaggagaa tttggcgtca agcgaacaat - 421 ggagaagatg caactgctgg tctcactcac atgatgatct ggcattccaa tctaaatgat - 481 gccacatacc agagaacaag agctctcgtg cgtactggga tggaccctag aatgtgctct - 541 ctgatgcaag gatcaactct cccgaggaga tctggagctg ctggtgcggc agtaaaggga - 601 gtcggaacga tggtgatgga actaattcgg atgataaagc gagggattaa cgatcggaat - 661 ttctggagag gtgaaaatgg gcgaagaaca agaattgcat atgagagaat gtgcaacatc - 721 ctcaaaggga aattccaaac agcagcacaa agagcaatga tggatcaggt acgggaaagc - 781 agaaatcctg ggaatgctga gattgaagat ctcatatttc tggcacggtc tgcactcatc - 841 ctgagaggat cagtggccca caagtcctgc ttgcctgctt gtgtgtacgg gcttgccgtg - 901 gccagtggat atgactttga gagagaaggg tactctctgg tcgggattga tcctttccgt - 961 ctgctgcaaa acagccaggt ctttagtcta attagaccaa atgagaatcc agcacataaa - 1021 agtcaattgg tgtggatggc atgccattct gcagcatttg aagatctgag agtctcaagc - 1081 ttcatcagag ggacaagagt ggccccaagg ggacaactat ctactagagg agttcaaatt - 1141 gcttcaaatg agaacatgga aacaatggac tccagcactc ttgaactgag aagcagatat - 1201 tgggctataa ggaccaggag tggaggaaac accaaccagc agagagcatc tgcaggacaa - 1261 atcagtgtgc agcctacttt ctcggtacag agaaatcttc ccttcgaaag agcgaccatt - 1321 atggcggcat tcacagggaa tacagagggc agaacatctg acatgaggac tgaaatcata - 1381 aggatgatgg aaagctccag accagaagat gtgtctttcc aggggcgggg agtcttcgag - 1441 ctctcggacg aaaaggcaac gaacccgatc gtgccttcct ttgacatgag taatgaagga - 1501 tcttatttct tcggagacaa tgcagaggaa tatgacaatt gaagaaaaat acccttgttt - 1561 ctact -// - diff --git a/config/reference_h5nx-all-time_ns.gb b/config/reference_h5nx-all-time_ns.gb deleted file mode 100755 index 400ad5c..0000000 --- a/config/reference_h5nx-all-time_ns.gb +++ /dev/null @@ -1,71 +0,0 @@ -LOCUS AF144307 865 bp RNA linear VRL 01-SEP-1999 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) nonstructural - proteins NS1 and NS2 (NS) gene, alternatively spliced products, - complete cds. -ACCESSION AF144307 -VERSION AF144307.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 865) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 865) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..865 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="genomic RNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 15..852 - /gene="NS" - CDS join(15..44,517..852) - /gene="NS2" - /note="NS2" - /codon_start=1 - /product="nonstructural protein 2" - /protein_id="AAD51931.1" - /translation="MDSNTITSFQDILQRMSKMQLESSSVDLNGMITQFERLKIYRDS - LGESMMRMGDLHSLQNRNATWRNELSQKFEEIRWLIAECRNILTKTENSFEQITFLQA - LQLLLEVESEIRTFSFQLI" - CDS 15..707 - /gene="NS1" - /note="NS1" - /codon_start=1 - /product="nonstructural protein 1" - /protein_id="AAD51930.1" - /translation="MDSNTITSFQVDCYLWHIRKLLSMRDMCDAPFDDRLRRDQKALK - GRGSTLGLDLRVATMEGKKIVEDILKSETNENLKIAIASSPAPRYITDMSIEEMSREW - YMLMPRQKITGGLMVKMDQAIMDKRIILKANFSVLFDQLETLVSLRAFTESGAIVAEI - FPIPSVPGHFTEDVKNAIGILIGGLEWNDNSIRASENIQRFAWGIHDENGGPSLPPKQ - KRYMAKRVESEV" -ORIGIN - 1 gtgacaaaga cataatggat tccaacacga taacctcgtt tcaggtagat tgttatctat - 61 ggcacataag aaagctactc agtatgagag acatgtgtga tgcccccttt gatgacaggc - 121 tccgaagaga ccaaaaggca ttaaagggaa gaggcagcac acttggactc gatttaagag - 181 tggctacaat ggaggggaaa aagatcgttg aggacatcct gaagagtgag acaaatgaaa - 241 acctcaaaat agccattgct tccagtcctg ctcctcggta tatcaccgat atgagcatag - 301 aggagatgag ccgagaatgg tacatgctga tgcctaggca gaaaataact ggaggcctta - 361 tggtgaaaat ggaccaagcc ataatggata aaagaattat ccttaaagca aatttctcag - 421 ttctatttga tcaactagag acattagtct ctctgagggc attcacagaa agtggtgcta - 481 ttgtggctga aatatttccc attccctccg taccaggaca ttttacagag gatgtcaaaa - 541 atgcaattgg aatcctcatc ggtggacttg aatggaatga taactcaatt cgagcgtctg - 601 aaaatataca gagattcgct tggggaatcc atgatgagaa tgggggacct tcactccctc - 661 caaaacagaa acgctacatg gcgaaacgag ttgagtcaga agtttgaaga gatcagatgg - 721 ctcattgctg aatgtagaaa tatactgaca aagactgaaa atagctttga acagataaca - 781 tttttgcaag cattgcaact cttacttgaa gttgagagtg agataaggac cttctctttt - 841 cagcttattt aatactaaaa aacac -// - diff --git a/config/reference_h5nx-all-time_pa.gb b/config/reference_h5nx-all-time_pa.gb deleted file mode 100755 index 4e97147..0000000 --- a/config/reference_h5nx-all-time_pa.gb +++ /dev/null @@ -1,91 +0,0 @@ -LOCUS AF144302 2233 bp RNA linear VRL 31-AUG-1999 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) polymerase (PA) - gene, complete cds. -ACCESSION AF144302 -VERSION AF144302.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 2233) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 2233) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..2233 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="genomic RNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 25..2175 - /gene="PA" - CDS 25..2175 - /gene="PA" - /codon_start=1 - /product="polymerase" - /protein_id="AAD51924.1" - /translation="MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEV - CFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEK - PKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKAD - YTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETVEERFEITGTMCRLADQS - LPPNFSSLEKFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPC - SQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNY - LLAWKQVLAELQDIENEEKIPKTKNMRKTSQLKWALGENMAPEKVDFEDCKDVSDLRQ - YDSDEPKPRSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV - SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFLIKGR - SHLRNDTDVVNFVSMEFSLTDPRLEPHRWEKYCVLRIGDMLLRTEIGQVSRPMFLYVR - TNGTSKIKMKWGMEMRRCPFQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGES - PKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFD - LGGLYEAIEECLINDPWVLLNASWFNSFLTHALR" -ORIGIN - 1 agcaaaagca ggtactgatc caaaatggaa gactttgtgc gacaatgctt caatccaatg - 61 attgtcgagc ttgcggaaaa ggcaatgaaa gaatatgggg aagatccgaa aatcgaaacg - 121 aacaaatttg ccgcaatatg cacgcactta gaagtctgtt tcatgtattc agatttccac - 181 tttattgatg aacggggcga atcaacaatt atagaatctg gcgatcccaa tgcattattg - 241 aaacaccggt ttgaaataat cgaagggagg gaccgaacaa tggcctggac agtggtgaat - 301 agtatctgca acaccacagg agttgagaag cctaaatttc tcccagattt gtatgactac - 361 aaggagaacc gatttattga aattggagtg acacggaggg aagttcacac atactatcta - 421 gaaaaagcca acaagataaa atctgagaag acacacattc acatattctc attcactgga - 481 gaggaaatgg ccaccaaagc ggactacacc cttgatgaag aaagcagggc ccgaatcaaa - 541 accaggctgt tcactataag gcaggaaatg gccagtaggg gtttatggga ttcctttcgt - 601 cagtccgaga gaggcgaaga gacagttgaa gaaagatttg aaatcacagg gactatgtgc - 661 aggcttgccg accaaagtct cccacctaat ttctccagcc ttgaaaaatt tagagcctat - 721 gtggatggat tcgaaccgaa cggctgcatt gagggcaagc tttctcaaat gtcgaaagaa - 781 gtaaacgcca gaattgagcc atttctgaag acaacaccac gccctcttag attacctgat - 841 gggcctccct gctctcagcg gtcgaagttt ttgctgatgg atgcccttaa attaagcatc - 901 gaagacccga gtcatgaggg ggaggggata ccgctatatg atgcaatcaa atgcatgaaa - 961 acatttttcg gctggaaaga gcccaacatt gtaaaaccac atgaaaaagg cataaacccc - 1021 aattacctcc tggcttggaa gcaggtgctg gcagagctcc aagatattga aaacgaggag - 1081 aaaattccaa agacaaagaa catgaggaaa acaagccaat tgaagtgggc acttggtgag - 1141 aatatggcac cagagaaagt agactttgag gattgcaaag atgttagcga tctaaggcag - 1201 tatgacagtg atgaaccaaa gcctagatca ctagcaagct ggatccagag tgaattcaac - 1261 aaggcatgcg aattgacaga ttcaagttgg attgaacttg atgaaatagg ggaagacgtt - 1321 gctccaattg agcacattgc aagtatgaga aggaactatt tcacagcgga agtatcccat - 1381 tgcagggcta ctgaatacat aatgaaggga gtgtacataa acacagcttt gttgaatgca - 1441 tcctgtgcag ccatggatga cttccaactg atcccaatga taagcaaatg cagaaccaaa - 1501 gaaggaagac ggaaaactaa cctgtatgga ttccttataa aaggaagatc ccatttgaga - 1561 aatgacaccg atgtggtaaa ctttgtgagt atggaattct ctcttactga tccgaggctg - 1621 gagccacaca gatgggaaaa gtactgcgtt cttcggatag gagacatgct cttacggact - 1681 gaaataggcc aagtgtcaag gcccatgttt ctttatgtga gaaccaatgg aacctccaag - 1741 atcaagatga aatggggcat ggaaatgagg cgatgccctt ttcaatccct tcaacagatt - 1801 gagagcatga ttgaggccga gtcttctgtc aaagaaaaag acatgactaa agaattcttt - 1861 gaaaacaaat cagaaacatg gccaattgga gaatcaccca agggagtgga ggaaggctcc - 1921 atcgggaagg tgtgcagaac cttactggct aaatctgttt tcaacagtct atatgcatct - 1981 ccacaactcg aggggttttc agctgaatca agaaaattgc ttctcattgt tcaggcactt - 2041 agggacaacc tggaacctgg aaccttcgat cttggggggc tatatgaagc aattgaggag - 2101 tgcctgatta atgatccctg ggttttgctt aatgcatctt ggttcaactc cttcctcaca - 2161 catgcactaa gatagttgtg gcaatgctac tatttgctat ccatactgtc caaaaaagta - 2221 ccttgtttct act -// - diff --git a/config/reference_h5nx-all-time_pb1.gb b/config/reference_h5nx-all-time_pb1.gb deleted file mode 100755 index 38f6893..0000000 --- a/config/reference_h5nx-all-time_pb1.gb +++ /dev/null @@ -1,94 +0,0 @@ -LOCUS AF144301 2341 bp RNA linear VRL 31-AUG-1999 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) polymerase (PB1) - gene, complete cds. -ACCESSION AF144301 -VERSION AF144301.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 2341) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 2341) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..2341 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="genomic RNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 25..2298 - /gene="PB1" - CDS 25..2298 - /gene="PB1" - /codon_start=1 - /product="polymerase" - /protein_id="AAD51923.1" - /translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN - RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI - FENSCLETMEVVQQTRVDKLTQGRQTYDWTLKRNQPAATALANTIEVFRSNGLTANES - GRLIDFLKDVMESMDKGEMEIITHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYL - IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN - EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR - NVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLASIDLKYFNESTRKKIEKI - RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALI - VNAPNHEGIEAGVDRFYRTCKLVGINMTKKKSYINRTGTCEFTSFFYRYGFVANFSME - LPSFGVSGINESADMSIGVTVIKNNMMDNDLGPATAQMALQLFIKDYRYPYRCHRGDT - QIQTRRSFELKKLWEQTRSKAGLLVSDGGPNPYNIRNLHIPEAGLKWELMDEDYQGRL - CNPLNPFVSHKEIESVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI - LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF - AEIMKICSTIEELGRQK" -ORIGIN - 1 agcaaaagca ggcaaaccat ttgaatggat gtcaatccga ctttactttt cttaaaagtg - 61 ccagcgcaaa atgctataag taccacattc ccttatactg gagatcctcc atacagccat - 121 ggaacaggaa caggatacac catggacaca gtcaacagaa cacatcaata ttcagaaaag - 181 gggaaatgga caacgaacac agagactgga gcaccccaac tcaatccgat tgatggacca - 241 ctacctgagg ataatgagcc gagtgggtat gcacaaacag attgtgtatt ggaagcaatg - 301 gctttccttg aagaatccca cccagggatc tttgaaaact cgtgtcttga aacgatggaa - 361 gttgttcagc aaacaagagt ggataagctg acccaaggtc gccaaaccta tgactggaca - 421 ttgaaaagaa accagccggc tgcaaccgct ttggccaaca ctatagaggt cttcagatcg - 481 aatggtctaa cagccaatga atcgggaagg ctaatagatt tcctcaaaga cgtgatggaa - 541 tcaatggata agggagaaat ggaaataata acacatttcc agagaaagag aagagtgagg - 601 gacaacatga ccaagaaaat ggtcacacaa agaacaatag ggaagaaaaa acaaaggctg - 661 aacaaaagga gctacctaat aagagcactg acactgaaca caatgacaaa agacgcagaa - 721 agaggcaaat tgaagaggcg ggcaattgca acacccggga tgcaaatcag aggattcgtg - 781 tactttgtcg aaacactagc gaggagtatc tgtgagaaac ttgagcaatc tggactcccc - 841 gtcggaggga atgaaaagaa ggctaaattg gcaaatgtcg tgaggaagat gatgactaac - 901 tcacaagata cagagctctc ttttacaatt actggagaca acaccaaatg gaatgagaat - 961 cagaaccctc ggatgtttct agcaatgata acatacatca caaggaacca acctgaatgg - 1021 tttagaaatg tcttaagcat tgctcctata atgttctcaa acaagatggc aagattaggg - 1081 aaaggataca tgttcgaaag taagagcatg aagctacgga cacaaatacc agcagaaatg - 1141 cttgcaagca ttgacttgaa atacttcaac gaatcaacga gaaagaaaat cgagaaaata - 1201 agacctctac taatagatgg cacagcctca ttgagtcctg gaatgatgat gggcatgttc - 1261 aatatgctga gtacagtctt aggagtttca atcctgaatc ttgggcagaa gaggtacacc - 1321 aaaaccacat actggtggga cggactccaa tcctctgatg atttcgctct catagtgaat - 1381 gcaccaaatc atgagggaat agaagcaggg gtggataggt tctataggac ttgcaaacta - 1441 gttggaatca atatgaccaa gaagaagtct tacataaatc ggacaggaac atgtgaattc - 1501 acaagcttct tctaccgcta tgggttcgta gccaacttca gtatggagct gcccagcttt - 1561 ggagtgtctg ggattaatga atcggctgac atgagcattg gtgttacagt gataaagaac - 1621 aatatgatgg acaacgacct tggaccagca acagctcaga tggctcttca gctattcatt - 1681 aaggactaca gatacccata ccgatgccac aggggggata cacaaatcca aacgaggaga - 1741 tcattcgagc tgaagaagct gtgggagcag acccgctcaa aggcaggact gttggtttca - 1801 gatggaggac caaacccata caatatccgg aatctccaca ttccggaggc tggcttgaag - 1861 tgggaattga tggatgaaga ctaccagggc agactgtgta atcctctgaa cccgtttgtt - 1921 agtcataagg aaattgagtc tgtcaacaat gctgtggtaa tgccagctca tggcccagcc - 1981 aagagcatgg aatatgatgc agttgcgact acacattcat ggattcccaa gaggaatcgt - 2041 tccattctca acaccagcca aagggggatt cttgaggatg aacagatgta tcagaagtgc - 2101 tgcaatctat tcgagaaatt cttccctagc agttcatatc ggaggccagt tggaatttcc - 2161 agcatggtgg aggccatggt gtctagggcc cgaattgatg cacgaattga cttcgagtct - 2221 ggaaggatta agaaagaaga gtttgctgag atcatgaaga tctgttccac cattgaagag - 2281 ctcggacggc aaaaatagtg aatttagctt gtccttcatg aaaaaatgcc ttgtttctac - 2341 t -// - diff --git a/config/reference_h5nx-all-time_pb2.gb b/config/reference_h5nx-all-time_pb2.gb deleted file mode 100755 index 85e790e..0000000 --- a/config/reference_h5nx-all-time_pb2.gb +++ /dev/null @@ -1,94 +0,0 @@ -LOCUS AF144300 2341 bp RNA linear VRL 31-AUG-1999 -DEFINITION Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) polymerase (PB2) - gene, complete cds. -ACCESSION AF144300 -VERSION AF144300.1 -KEYWORDS . -SOURCE Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - ORGANISM Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) - Viruses; ssRNA viruses; ssRNA negative-strand viruses; - Orthomyxoviridae; Influenzavirus A. -REFERENCE 1 (bases 1 to 2341) - AUTHORS Xu,X., Subbarao, Cox,N.J. and Guo,Y. - TITLE Genetic characterization of the pathogenic influenza - A/Goose/Guangdong/1/96 (H5N1) virus: similarity of its - hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks - in Hong Kong - JOURNAL Virology 261 (1), 15-19 (1999) - PUBMED 10484749 -REFERENCE 2 (bases 1 to 2341) - AUTHORS Xu,X., Subbarao,K., Cox,N.J. and Guo,Y. - TITLE Direct Submission - JOURNAL Submitted (20-APR-1999) Influenza Branch, Center for Diseases - Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA -FEATURES Location/Qualifiers - source 1..2341 - /organism="Influenza A virus - (A/goose/Guangdong/1/1996(H5N1))" - /mol_type="genomic RNA" - /strain="A/Goose/Guangdong/1/96(H5N1)" - /db_xref="taxon:93838" - gene 28..2307 - /gene="PB2" - CDS 28..2307 - /gene="PB2" - /codon_start=1 - /product="polymerase" - /protein_id="AAD51922.1" - /translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA - LRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN - GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQ - DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL - PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADP - LASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTN - GSSVKKEEEVLTGNLQTLKIKVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQ - SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG - IEPIDNVMGMIGILPDMTPSAEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQQ - GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQ - DPTMLYNKMEFESFQSLVPKAARSQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA - PPEPSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEG - TAGVESAVLRGFLILGREDKRYGPALSINELSNLAKGEKANVLIMQGDVVLVMKRKRD - FSILTDSQTATKRIRMAIN" -ORIGIN - 1 agcaaaagca ggtcaattat attcaatatg gaaagaataa aagaactaag agatctaatg - 61 tcgcagtccc gcactcgcga gatactaaca aaaaccactg tggatcatat ggccataatc - 121 aagaaataca catcaggaag acaagagaag aaccctgctc tcagaatgaa atggatgatg - 181 gcaatgaaat atccaatcac agcagacaag agaataatgg agatgattcc tgaaaggaat - 241 gagcaaggac aaacgctttg gagcaagaca aatgatgctg ggtcggacag agtgatggtg - 301 tctcccctag ctgtaacttg gtggaacagg aatgggccga caacaagtac agtccattat - 361 ccaaaggttt acaaaacata ctttgagaag gttgaaaggt taaaacatgg aaccttcggt - 421 cccgttcatt tccgaaacca agttaaaata cgtcgccggg tggatataaa cccgggccat - 481 gcagatctca gtgctaaaga agcacaagat gttatcatgg aggtcgtttt cccaaatgaa - 541 gtgggagcta gaatattgac atcagagtcg caattgacaa taacaaaaga gaagaaagaa - 601 gagctccagg attgtaaaat tgctccttta atggtggcat acatgttgga aagagaactg - 661 gtccgcaaaa ccagatttct accggtagca ggcggaacaa gcagtgtgta cattgaggta - 721 ttgcatttga ctcaagggac ctgttgggaa cagatgtaca ctcccggcgg agaagtaaga - 781 aatgatgatg ttgaccagag tttgatcatc gctgccagaa acattgttag gagagcaaca - 841 gtatcagcgg acccactggc atcactcttg gagatgtgtc acagcacaca aattggggga - 901 ataaggatgg tggacatcct taggcaaaac ccaactgagg agcaagctgt ggatatatgc - 961 aaagcagcaa tgggtttgag gatcagttca tcctttagct ttggaggctt cactttcaaa - 1021 agaacaaatg gatcatccgt caagaaggaa gaggaagtgc ttacaggcaa cctccaaaca - 1081 ttgaaaataa aagtacatga ggggtatgaa gaattcacaa tggttgggcg gagagcaaca - 1141 gctatcctga ggaaagcaac tagaaggctg attcagttga tagtaagtgg aagagatgaa - 1201 caatcaatcg ctgaagcgat cattgtagca atggtgttct cacaggagga ttgcatgata - 1261 aaggcagtcc gaggcgatct gaatttcgtg aacagagcaa accaaagatt gaaccccatg - 1321 catcaactcc tgaggcactt ccaaaaagat gcaaaagtgc tgtttcagaa ctggggaatt - 1381 gaacctattg acaatgtcat ggggatgatc ggaatattac ctgacatgac tccaagcgca - 1441 gagatgtcac tgagaggagt gagagttagt aagatgggag tagatgaata ttccagcacg - 1501 gagagagtgg tggtgagtat tgaccgtttc ttgagggtcc gagatcagca ggggaacgta - 1561 ctcttatctc ctgaagaggt tagtgaaaca cagggaacag agaagttgac aataacatat - 1621 tcatcctcaa tgatgtggga aatcaacggt cctgagtcag tgcttgttaa cacttatcaa - 1681 tggatcatca ggaattggga gactgtaaag attcaatggt ctcaagatcc cacaatgctg - 1741 tacaataaga tggagtttga atcgttccaa tccttggtgc caaaggctgc cagaagccaa - 1801 tatagtggat ttgtgagaac actattccaa cagatgcgtg atgttttggg gacatttgat - 1861 actgtccaaa taatcaagct gctaccattt gcagcagccc caccggagcc gagcagaatg - 1921 cagttttctt ctctaactgt gaatgtgaga ggctcaggaa tgagaatact cgtgaggggt - 1981 aactcccccg tgttcaacta caacaaggca accaaaaggc ttacagtcct cggaaaggac - 2041 gcaggtgcat taacagaaga tccagacgag ggaacagccg gggtggaatc tgcagtattg - 2101 aggggattcc taattctagg cagagaggac aaaagatatg gacccgcatt gagcatcaat - 2161 gaactgagca atcttgcaaa aggggagaag gctaatgtat tgataatgca aggagacgtg - 2221 gtgttggtaa tgaaacggaa acgggacttt agcatactta ctgacagcca gacagcgacc - 2281 aaaagaattc ggatggccat caattagtgt tgaatagttt aaaaacgacc ttgtttctac - 2341 t -// -