2250 days ago
Perl script to find coding regions in DNA sequences
..."\U$seq"; # we are going to use the array @codons to store all of the codons in # the input DNA sequence. To split the sequence in segments of length # three, a regular expressio...2195 days ago
Biological Sequence handling with Perl !
...} # These methods probably don't have to be overridden # The length of the sequence sub length { my $self = shift;...ift; return (__PACKAGE__ . '::Subsequence')->new($self,$self->length,1); } sub translate { my...2221 days ago
Perl script to count number of Ns in a multifasta file !
...; open(I,$ARGV[0]) or die($!); while(){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\...2184 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...} else { chomp $line; $sequences{$seqid}{seq} .= $line; $sequences{$seqid}{len} += length $line; $sequence...2180 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 here...2180 days ago
2166 days ago
Perl script to find palindromic pattern !
...rnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; }; chomp $in; print $in; for my $p1 ( 1 .. length( $in ) -2 ) { next unles...2139 days ago
2115 days ago
Perl script to extract a sequence from multifasta with range !
...chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = shift @chunk; my $seqlen = length join "", @chunk; pri...2106 days ago