Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
#!/usr/local/bin/perl -w # While executing this script it asks for the file name...ith the path. In windows: c:\dnafile.txt, In Linux: /ho...es not exist!!! \n"; print "Cannot open file \"$dna_filenam...$base eq 't' ) { ++$count_of_T; } els...2915 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use stri...eturnType => undef, maxRecords => undef, format...$param{query}"; my $esearch_result = get($esearch);...le} ) or die("Error: Cannot open $param{outputFile}...2915 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w ##########################...# #MLP neural network in Perl Original source code by Phil Brierley #Translated into perl - ccolbourn Oct 2004 ###########...output neuron #To include an input bias create an #extra input in the...2915 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Uti...'', $outputfile; my $size = 21; my $count = 10; while (my $line = ) { next unless $line =~ /^([ATGCN]+)/; my $genome =...2914 days ago
2909 days ago
Blast result parser with Perl and Bioperl
...ibuted under GNU General Public License. # This script will parse a NCBI blastx...ing results are reported: # accesion number, length, descrip...rt\thit_end\tpositives\tidentical\n"; # extraction of info...my $hspcount = 0;...2913 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...help\n". " -m: missing character\n". "Print out the name of sequences with characters other than ATGC-.\n"...place ? to the ambigous characters.\n" . "If multiple f...#@seqArr = sort { $a->id() cmp $b->id() } @seqArr; fore...2913 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2913 days ago
2913 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";2913 days ago