Echinoderm_Regeneration ¹

Summer Internship project at the Univeristy of North Carolina at Charlotte.

Overview²

Sea Cucumber Genome Project

• • Literature Review
• • Fastqc, Trimmomatic, Star and Braker Scripts and Results
• • De novo ABySS assemblage, Exonerate Alignment Scripts and Results

Genome Assembly Convert and Capture (GTF Convert)

• • Series of scripts that converters and integrates results from different aligners and clusteres (BLAST, exonerate, and CD-HIT) to GTF format file.

Annotation

• • Acquisition of Gene Annotations and Alignment against cannonical sequences in model organisms and other Echinoderms.
• • Referenced against uniprot and ncbi

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Delta-Notch and Wnt pathways in the context of Drosophila Melanogaster

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NOTCH

Domain	blastn	blastp	CDHIT	Exonerate (unfiltered)
hairless	10	9	3	47
notch1	14	20	8	33
adam	17	11	8	59
p300	23	21	12	60
nack	20	20	8	44
modifiers	18	7		70
mindbomb	8	4	4	22
nack	7	5	5	40
hes	6	6	3	17
csl	12	8	7	47
gammas_secretase	8	8	4	43

WNT

Domain	blastn	blastp	CDHIT	Exonerate (Unfiltered)
znrf3	17	14	6	30
wls	22	20	3	18
tspan12	5	2	1	19
tcf	7	7	3	107
sfrp	6	5	1	33
sclerostin	14	13	2	25
rnf43	9	7	2	29
r-spondin	14	10	3	41
porcupine	4	4	2	29
notum	16	15	6	39
norin	8	6	4	7
kremen	8	8	4	17
lgr5	15	11	6	55
gsk3	9	7	3	26
groucho	7	7	3	35
dishevelled	13	10	2	41
geta-catenin	7	4	6	13
ck1	18	13	4	49
axin	14	10	3	18
apc	8	9	4	38
frizzled	10	8	3	33

Processing

1. Exonerate, CDHIT and BLAST Outputs converted independently for parsing into multifasta
2. Multi-GTF Aggregate filtered for nonredundant hits.
3. NCBI CDD Hits parsed for canonical domains and ascensions.

Notes:

Footnotes

1. This is an ongoing repository that will be archived in May 2023. ↩

2. WIPs remain unchecked. ↩