2926 days ago
Blast result parser with Perl and Bioperl
...on, E value, bit score, query frame, query start, query end, hit start, hit end, positives, and iden...cription\tE value\tbit score\tframe\tquery_start\t"; print OUT "query_end\thi...# get the start and the end of the query sequ...2923 days ago
2919 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. ed. CUP 1998, Pg. 19 # Needleman...2915 days ago
Count GC Content in nucleotide sequence with Perl
...\tT Count\n"; $seq = ""; while () { chomp; if (/^>/) { #finish up previous line. if (length($seq) > 0) { &process_it; } #start new line. $id = $_; $id =...2915 days ago
2702 days ago
Calculate ATGC percentage in parallel with perl
...ent just got out of the pool ". "with PID $pid and exit code: $exit_code\n"; } ); $pm->run_on_start( sub { my ($pid,$ident)=@_; #print "** $ident started, pid: $pid\n"; } );...2665 days ago
Extracting FASTA sequences based on position with perl script !!
...nput.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; w...le () { chomp; next unless /(.+)/; my ($header) = "$/$1_$start-$end\n"; my $seq = ${^PO...2631 days ago
Genetic Algorithms demonstration with word DNA in Perl
...pulation my $popsize = 1024; # a good starting point my $dna_length = 51...parent > 0 my $individual = undef; # start with an undefined individual...to_words($dna); my $fitness = 0; # start with 0 fitness my $max_ent...2381 days ago
Plot the clock using Lastz -gerenal outfile
...se warnings; use Statistics::R ; use List::Util qw(sum); #Usage perl clockPlot.pl Palindrome.palfc 1500 my $R = Statistics::R->new() ; $R->startR ; my $fileN=$ARGV[0]; my...2308 days ago