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...ile.txt, In Linux: /home/user/sequence/dnafile.txt print...E; $DNA = join( '', @DNA); print " \n The original DNA file...} else { print "Error - Unknown base: $ba...2906 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com)...database => undef, returnType => undef, maxRe...$param{returnType} = lc( $param{returnType} ); $param{qu..."Retrieving $param{maxRecords} records out of...2906 days ago
A multilayer perceptron (MLP) neural network in Perl
...#################### #MLP neural network in Perl Original source code by Phil Brierley #Tra...######## #Tanh hidden neurons #Linear output neuron...$numInputs = 3; my $numPatterns = 4; ###################...he data initData(); # train the network for(my $j...2906 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Util qw/ shuffle /; my $outputfile = 'randomoutput.txt'; open my $...my $len_genome = length $genome; my @start_points = shuffle(0 .. $len_g...2905 days ago
2900 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU Gen...# For each hit, the following results are reported: # accesi...tdescription\tE value\tbit score\tframe\tquery_start\t"; pri...t the E value of the hit print OUT $hit->significance . "...2904 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n"....s specified, the ambiguous characters are repleced with the\n...re marged. If no \n". "argument is given, it will take...$a->id() cmp $b->id() } @seqArr; foreach my $s (@seqArr)...2904 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2904 days ago
2904 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";2904 days ago