GitHub - answer19831020/ltr-finder: Automatically exported from code.google.com/p/ltr-finder

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Automatically exported from code.google.com/p/ltr-finder

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Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
tRNA		tRNA
test		test
BooleanString.C		BooleanString.C
BooleanString.h		BooleanString.h
CallPsScan.cpp		CallPsScan.cpp
CallPsScan.h		CallPsScan.h
LinearSuffixSort.cpp		LinearSuffixSort.cpp
LinearSuffixSort.h		LinearSuffixSort.h
PBS.cpp		PBS.cpp
PBS.h		PBS.h
PairsFilter.cpp		PairsFilter.cpp
PairsFilter.h		PairsFilter.h
Timing.C		Timing.C
Timing.h		Timing.h
check_result.pl		check_result.pl
down_tRNA.pl		down_tRNA.pl
filter_rt.pl		filter_rt.pl
genome_plot.pl		genome_plot.pl
genome_plot2.pl		genome_plot2.pl
genome_plot_svg.pl		genome_plot_svg.pl
lcp.c		lcp.c
lcp.h		lcp.h
main.cpp		main.cpp
makefile		makefile
psearch.cpp		psearch.cpp
readme.txt		readme.txt
reformat.sh		reformat.sh
regex.c		regex.c
regex.h		regex.h
seq.c		seq.c
seq.h		seq.h
stdaln.c		stdaln.c
stdaln.h		stdaln.h
stdaln_interface.cpp		stdaln_interface.cpp
stdaln_interface.h		stdaln_interface.h
struct.h		struct.h
tags		tags

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useful usage:
link ltr_finder and genome_plot.pl
./ltr_finder TestSet/yeast.fa -PCHR10 -w2 -f /dev/stderr 2>&1 >fig_test/result.txt | perl genome_plot.pl fig_test/

algorithm
get pair
join pair(also cut at possible gap)
extend pair
find edge
find TG..CA and TSR
find signal(find PBS and PPT)
find RT
find IN(core) IN(c-term) RH(if -a)
output with restrict

can read multi sequence now
predict domains
modify SuffixArray function, no longer change input string
stdaln can handle NNNN vs atcg
delete exact match pairs that contain Ns

fix bug:
handle 'NNNNNNN' before local_align