Results for "UP"
Bio-Scripts
Retrieve NCBI GenBank records with a range of accession numbers
...es} >= $param{maxRetries} ) { die("Too many failures--giving up search."); }...>= $param{maxRetries} ) { die("Too many failures--giving up search."); }...2929 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-Wunsch global...2918 days ago
Count GC Content in nucleotide sequence with Perl
...Count\n"; $seq = ""; while () { chomp; if (/^>/) { #finish up previous line. if (length($...OUT "$id\t"; } else { $seq = $seq . $_; } } #finish up last line. &process_it; c...2918 days ago
- ...l(matrix[,x],97.5) - single column from a normal distribution #USAGE: CI_tdist(matrix[,x],97.5) - single column from a t distribution #Created and updated by Santhilal Subhash on...
2884 days ago
- ...is a title to place in the output. default: null -- no title appears If for some reason this program is disrupted during a run, restart wit...
2706 days ago
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->ne...2703 days ago
Perl script to insert the DNA string in genome
...ry_id eq $chr){ my $length = length($seq->seq); my $upstream=substr($seq->seq, 0, $p...seq, $pos,$length); my $seq_obj = Bio::Seq->new(-seq => $upstream.$seqI.$downstream,-disp...2672 days ago
Calculate ATGC percentage in parallel with perl
...es; # hash to resolve PID's back to child specific information my $pm = new Parallel::ForkManager($max_procs); # Setup a callback for when a child finishes up so we can # get it's exit...2669 days ago
- ...or normal overlaps my ($lower, $upper) = (40, 100); for my $n...s_between = (sort {$a $b} $lower, $upper, $num)[1] == $num;...rnings; use 5.010; my ($lower, $upper) = (40, 100); for my $r...ntf "[@$range] is%s within [$lower $upper]\n", $is_within ? "" : " n...
2649 days ago
Genetic Algorithms demonstration with word DNA in Perl
...chomp; } # eliminate words over $max_entry_length letters, and uppercase them @dictionary =...onary; # build the letter frequencies hash (remember, all letters are uppercase) $freqs{$_}++ fore...2384 days ago
