Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2117 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower tha...coding protein sequences and low values (zero or even negative) for intronic regions. exon.fa >HUMHBB.2ex...2118 days ago
2038 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict;...ses are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stores a hash from the contig...$end=$i; my $ini=$end-$n+1; push(@regions,"$ini $end"); } $n=0;...2026 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we hav...1328 days ago
Identify genome-wide synteny with LASTZ alignment
#This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alig...s chr1.chain.filter.tnet chr1.chain.filter.qnet netSyntenic chr1.chain.filter.tnet chr1.c...r1.chain.filter.tnet.synnet.axt.maf Step 3: Get synteni...480 days ago