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, '2170 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2255 days ago
2226 days ago
Biological Sequence handling with Perl !
...unless $sequence->can('seq'); %{$self} = %{$sequence}; # clone operation } else { croak "D...urn (__PACKAGE__ . '::Subsequence')->new($self,$self->length,1); } sub translate { my $self = shift;...2197 days ago
Perl script to find coding regions in DNA sequences
...tableofcodons) do while ($line = ) { # extract the two values or columns w...seql = ; # load the complete sequence into an array my $seq = ""; # u...log must be applied to obtain the log-likelihood ratio. # It is recommended the...2171 days ago
2167 days ago
2160 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...$cnt]\n$refSeq->{@$SeqIds[$cnt]}{seq}\n"; close $ofh or die "Could not close file '$tmpFile' $!"; $cnt++; system ("mafft --retree 1 --maxiterate 0 --thread 40 $tmpFile > MA...2156 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2156 days ago
Perl script to convert GFF 2 FASTA !
...upstream3000.fasta" ); ###### Output type description ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of i...2155 days ago