Blast result parser with Perl and Bioperl
...it start, hit end, positives, and identical # The results are...) { # the name of the query sequence print OUT $result->query...# the length of the query sequence print OUT $result->quer...# get the start and the end of the query sequence...2914 days ago
2914 days ago
Perl to print indivisual nucleotide from a sequence!
#!/usr/bin/perl use strict; use warnings; my $string = "ATGCTTGCGT?AAATG??CT?GCGTA"; my @chars = split("", $string); print "First character: $chars[0]\n";2914 days ago
2910 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. e...usage: $0 \n" unless @ARGV == 4; # get sequences, matrix and gapcost from command line...2906 days ago
Count GC Content in nucleotide sequence with Perl
#!/usr/bin/perl -w ### Usage: get_gc_content.pl ### #------------------------------------------------------...2906 days ago
Implementation of biological random mutation with Perl
#!/usr/bin/perl -w use strict; use warnings; #sequence for a better recognition my $DNA="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA \ n"; my $I; my $mutant; srand (time...2901 days ago
Perl script to generate a random psuedo DNA sequence !
#!/usr/bin/perl print "Enter a number of nucleotides: \n"; chomp ($N = ); @b=qw/A T G C/;print ">Genome\n";while($l2883 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extractSe...2875 days ago
Perl script introduces control structures, arrays and hashes.
#!/usr/bin/env perl use strict; use warnings; my @first_array = ('DNA', 'ATGCGTGC...umber of seqs' => 2 ); print $sequence{'DNA'}, "\n"; # Control Loop: foreach foreach my $key (sort (keys %sequence)...2862 days ago