Count the frequency of base G in a given DNA sequence
...; my $DNA = "GATTACACAT"; #initialize $countG and $currentPos my $countG = 0; my $currentPos = 0; #calculate the length...if it is the base G #if 'yes' increment $countG while($currentPos < $DNAlength){ my $base = s...2917 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqIO->newFh('-file...2916 days ago
Perl script to Mutate a DNA Sequence
..."Cannot open file \"$dnafilename\"\n\n"; goto h; } my $DNA = ; close DNAFILE; my $i; my $muta...$mutant\n"; } sub mutate { my($dna) = @_; my($position) = randomposition($dna);...2916 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
..."; print "Cannot open file \"$dna_filename\"\n"; die; } @DNA = ; close DNAFILE; $DNA = join( '', @...++$errors; } } print "Adenine = $count_of_A\n"; print "Cytosine = $count_of_C\n"; print "...2916 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...format => undef, verbose => undef, url...' => \$param{maxRecords}, 'verbose|v' => \$param{verbose}...= uri_escape( $param{query} ); _doSearch(%param); sub _doSearc...{ message( $param{verbose}, "Retrievi...2916 days ago
2910 days ago
Blast result parser with Perl and Bioperl
...me, query start, query end, hit start, hit end, positives, and identical # The...\t"; print OUT "query_end\thit_start\thit_end\tpositives\tidentical\n"; # ext...last if ($count == $numHits); } } } close OUT; print " DONE!!!\n";2915 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2915 days ago
2915 days ago
2909 days ago