Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fas...eq => $upstream.$seqI.$downstream,-display_id => $seq->primary_id,-alphabet => "dna"...2659 days ago
Calculate ATGC percentage in parallel with perl
#!/usr/bin/perl use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage: perl testParall...y is out of the pool!\n"; sub checkATCG { my $name=shift; my $DNA=$sequences{$name}; my $length=length $DNA;...2656 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...2650 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512 bits) use strict; use...# a good starting point my $dna_length = 512; # 4 "letters" in the DNA my $dna_byte_length = $dna_length / 8...ent => 0, fitness => 0, dna => 0 }; # this is breeding...2372 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted...2314 days ago
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, '2155 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input argum...if (scalar(@ARGV) < 2) { print "dnaloglkh.pl codontable DNAsequence\n"; exit(1); }...S,"< $filecodontable")) { print "dnaloglkh.pl: the file $filecodon...####################### # open the DNA s...2155 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; use...elf->{'type'} = $type || ($sequence=~/u/i ? 'RNA' : 'DNA'); } return $self; }...self->{'type'} = $_[0] : $self->{'type'}; } sub is_DNA {...2181 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::Seq...">$ARGV[2].pep.fasta" ); my $outfile_cdna = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene =...ending with a stop codon included) # cdna -...2139 days ago
2061 days ago