v1

.gitattributes

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+data/ecoli_trna_scan.tar filter=lfs diff=lfs merge=lfs -text
+data/k2_subset_with_rfam_consensus.tar filter=lfs diff=lfs merge=lfs -text
+data/k2.tgz filter=lfs diff=lfs merge=lfs -text
+data/README filter=lfs diff=lfs merge=lfs -text
+data/Rfam_local.tar filter=lfs diff=lfs merge=lfs -text
+data/rfam_pool.fa filter=lfs diff=lfs merge=lfs -text
+data/semi_global_pvalue.tar filter=lfs diff=lfs merge=lfs -text
+examples/ecoli_MG1655.fa filter=lfs diff=lfs merge=lfs -text
+examples/RF00167_1_nogap.ref filter=lfs diff=lfs merge=lfs -text
+examples/RF00167_1.raw filter=lfs diff=lfs merge=lfs -text
+examples/RF00167_1.ref filter=lfs diff=lfs merge=lfs -text
+examples/trna.fa filter=lfs diff=lfs merge=lfs -text
+examples/tRNAscan.fa filter=lfs diff=lfs merge=lfs -text

src/Makefile

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+CXX             = g++ 
+#CXXFLAGS        = -g -DDEBUG
+LDFLAGS        = -L. -lm -lRNA
+all: RNAmountAlignScan RNAmountAlign
+
+RNAmountAlignScan: RNAmountAlignScan.o pair_align.o arguments.o aux.o mountain_height.o evd.o stats.o karlin_altschul.o
+	${CXX} ${CXXFLAGS} -o RNAmountAlignScan RNAmountAlignScan.o pair_align.o arguments.o aux.o mountain_height.o evd.o stats.o karlin_altschul.o ${LDFLAGS}
+
+RNAmountAlign: RNAmountAlign.o pair_align.o arguments.o aux.o mountain_height.o stats.o karlin_altschul.o evd.o multi_align.o profile.o profile_aligner.o 
+	${CXX} ${CXXFLAGS} -o RNAmountAlign RNAmountAlign.o pair_align.o arguments.o aux.o mountain_height.o stats.o karlin_altschul.o evd.o multi_align.o profile.o profile_aligner.o ${LDFLAGS}
+
+RNAmountAlignScan.o:RNAmountAlignScan.cpp RNAmountAlignScan.h arguments.h pair_align.h mountain_height.h aux.h evd.h stats.h karlin_altschul.h
+	${CXX} ${CXXFLAGS} -c RNAmountAlignScan.cpp
+
+RNAmountAlign.o:RNAmountAlign.cpp arguments.h pair_align.h mountain_height.h aux.h
+	${CXX} ${CXXFLAGS} -c RNAmountAlign.cpp
+
+pair_align.o:pair_align.cpp aux.h aux.cpp
+	${CXX} ${CXXFLAGS} -c pair_align.cpp
+
+arguments.o:arguments.cpp aux.h
+	${CXX} ${CXXFLAGS} -c arguments.cpp 
+
+aux.o:aux.cpp pair_align.cpp
+	${CXX} ${CXXFLAGS} -c aux.cpp
+
+mountain_height.o:mountain_height.cpp
+	${CXX} ${CXXFLAGS} -c mountain_height.cpp
+
+stats.o:stats.cpp stats.h
+	${CXX} ${CXXFLAGS} -c stats.cpp
+
+evd.o:evd.cpp evd.h
+	${CXX} ${CXXFLAGS} -c evd.cpp
+
+karlin_altschul.o: karlin_altschul.cpp karlin_altschul.h
+	${CXX} ${CXXFLAGS} -c karlin_altschul.cpp
+
+multi_align.o:multi_align.cpp multi_align.h aux.h profile_aligner.h profile_aligner.h pair_align.h
+	${CXX} ${CXXFLAGS} -c multi_align.cpp
+
+profile_aligner.o:profile_aligner.cpp profile_aligner.h aux.h aux.cpp profile_aligner.h profile_aligner.cpp
+	${CXX} ${CXXFLAGS} -c profile_aligner.cpp
+
+
+profile.o:profile.cpp profile.h aux.h aux.cpp
+	${CXX} ${CXXFLAGS} -c profile.cpp
+
+clean:
+	rm -fr *.o RNAmountAlignScan RNAmountAlign

src/README.txt

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+Amir Bayegan, Peter Clote --Boston College
+
+/******************************************************************************
+ *   Copyright (C) 2018  Amir Bayegan, Peter Clote                            *
+ *                                                                            *
+ *  This program is free software: you can redistribute it and/or modify      *
+ *  it under the terms of the GNU General Public License as published by      *
+ *  the Free Software Foundation, either version 3 of the License, or         *
+ *  (at your option) any later version.                                       *
+ *                                                                            *
+ *  This program is distributed in the hope that it will be useful,           *
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of            *
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             *
+ *  GNU General Public License for more details.                              *
+ *                                                                            *
+ *  You should have received a copy of the GNU General Public License         *
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.     *
+ ******************************************************************************/
+
+RNAmountAlign performs a local/semi-global/global sequence structure alignment. 
+
+RNAmountAlignScan executable is used for searching a query in a given target sequence.
+
+Statistics are reported based on the alignment type either from Karlin-Altschul
+or parameter fitting(see the paper).
+
+
+Running the program:
+
+Executables:
+	RNAmountAlign
+	RNAmountAlignScan
+
+WARNING: The current libRNA.a is compiled for Linux systems. 
+		 If there is a problem with linking the library, please download
+		 and compile Vienna RNA Package on your system and replace 
+		 the current libRNA.a with the one obtained from Vienna.
+
+Usage: ./RNAmountAlign [options]
+REQUIRED:
+	RNAmountAlign:
+		-f <string>	the input fasta file containing two sequences 
+		OR
+		-s <string> <string> provide sequence1 and sequence2
+
+
+OPTIONS:
+
+ALIGNMENT:
+	-gi <float>	Gap initiation penalty for sequence alignment(Default:-3).
+			A negative value should be provided
+
+	-ge <float>	Gap extension penalty for sequence alignment(Default:-1).
+			A negative value should be provided
+
+	-gamma <float>	Weight of the structural homology. Must be in [0,1](Default:0.5)
+			similarity = gamma*str_sim + (1-gamma)*seq_sim
+
+	-m <string>	Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat)
+			All RIBOSUM files are included in ./matrices directory
+
+	-semi 		Perform semi-global alignment.
+			Both gap ends of the firts sequence will be free of penalty.
+
+	-local 		Perform local alignment
+
+	-global 		Perform global alignment.(Default alignment type)
+
+	-alifold		Output the consensus structure of the alignment from RNAalifold
+
+
+STATISTICS:
+		KA=Karlin-Altschul; EVD=extreme value dirstribution, ND=normal distribution
+
+	-stat		Report statistics based on the alignment type(Default: off). 
+			For local alignments: E-value from Karlin-Altschul(default) or EVD fitting
+			For global alignments: p-value from ND fitting
+			For semi-global alignments: p-value from ND fitting
+
+	-evd		EVD fitting will be used for local alignments instead of KA
+
+	-num <int>	Number of random sequences generated for fitting.(Default:500)
+
+	-gc <int>	Size of GC bins (an integer between [0-100]). (Default: 5)
+			This is used only with with parameter fitting and not KA.
+
+
+OUTPUT:
+	-o <string>	Write the output to a file.
+			If not used the output will be printed to stdout.
+
+	-format <clustal|fasta>	Format of the alignment output. (Default: clustal)
+
+	-v		Verbose output. Prints MFE structures, the ensmeble expected and incremental heights.
+
+	-h		Print help
+
+/********************************************************************************
+
+Usage: ./RNAmountAlignScan [options]
+REQUIRED:
+	RNAmountAlignScan:
+		-qf <string>	fasta file containing query sequence
+		AND
+		-tf <string>	fasta file containing target sequence
+
+
+OPTIONS:
+
+SLIDING
+	 -window <int>	Size of the sliding window(Default:300).
+
+	 -step <int>	Step size for incrementing the window start(Default:200).
+
+
+ALIGNMENT:
+	-gi <float>	Gap initiation penalty for sequence alignment(Default:-3).
+			A negative value should be provided
+
+	-ge <float>	Gap extension penalty for sequence alignment(Default:-1).
+			A negative value should be provided
+
+	-gamma <float>	Weight of the structural homology. Must be in [0,1](Default:0.5)
+			similarity = gamma*str_sim + (1-gamma)*seq_sim
+
+	-m <string>	Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat)
+			All RIBOSUM files are included in ./matrices directory
+
+	-semi 		Perform semi-global alignment.
+			Both gap ends of the firts sequence will be free of penalty.
+
+	-local 		Perform local alignment
+
+	-global 		Perform global alignment.(Default alignment type)
+
+
+STATISTICS:
+		KA=Karlin-Altschul; EVD=extreme value dirstribution, ND=normal distribution
+
+	-stat		Report statistics based on the alignment type(Default: off). 
+			For local alignments: E-value from Karlin-Altschul or EVD fitting
+			For global alignments: p-value from ND fitting
+			For semi-global alignments: p-value from ND fitting
+
+	-evd		EVD fitting will be used for local alignments instead of KA
+
+	-num <int>	Number of random sequences generated for fitting.(Default:500)
+
+	-gc <int>	Size of GC bins (an integer between [0-100]). (Default: 5)
+			This is used only with with parameter fitting and not KA.
+
+
+OUTPUT:
+	-o <string>	Write the output to a file.
+			If not used the output will be printed to stdout.
+
+	-format <clustal|fasta>	Format of the alignment output. (Default: clustal)
+
+	-v		Verbose output. Prints MFE structures, the ensmeble expected and incremental heights.
+	-h		Print help