Perl script to insert the DNA string in genome
...>seq, $pos,$length); my $seq_obj = Bio::Seq->new(-seq => $upstream.$seqI.$downstream,-display_id => $seq->primary_id,-alphabet => "dna" ); $seq_out->wr...2643 days ago
Calculate ATGC percentage in parallel with perl
...ldren...\n"; $pm->wait_all_children; print "Everybody is out of the pool!\n"; sub checkATCG { my $name=shift; my $DNA=$sequences{$name}; my $length=length $DNA; my $a=($DNA=~tr/A//); my $...2640 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', -file =>...2634 days ago
Genetic Algorithms demonstration with word DNA in Perl
...# 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...calculate the fitness of the DNA sub fitness { my $dna =...2356 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 sorte...2298 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, '2139 days ago
Perl script to find coding regions in DNA sequences
...error if (scalar(@ARGV) < 2) { print "dnaloglkh.pl codontable DNAsequence\n"; exit(1); }...ROPCODONS,"< $filecodontable")) { print "dnaloglkh.pl: the file $filecodon...############################### # open the DNA sequence (second file) if...2139 days ago
Biological Sequence handling with Perl !
...($sequence); $self->{'type'} = $type || ($sequence=~/u/i ? 'RNA' : 'DNA'); } return $self; }...n defined($_[0]) ? $self->{'type'} = $_[0] : $self->{'type'}; } sub is_DNA { my $self = shift;...2165 days ago
Perl script to convert GFF 2 FASTA !
...-file => ">$ARGV[2].pep.fasta" ); my $outfile_cdna = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene =...ATG and ending with a stop codon included) # cdna - transcribed sequence (devoi...2123 days ago
2044 days ago