Results for "OS"
Bio-Scripts
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...2909 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"; $in = Bio::SeqIO->newFh('-file...2908 days ago
Perl script to Mutate a DNA Sequence
..."Cannot open file \"$dnafilename\"\n\n"; goto h; } my $DNA = ; close DNAFILE; my $i; my $muta...$mutant\n"; } sub mutate { my($dna) = @_; my($position) = randomposition($dna);...2908 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
..."; print "Cannot open file \"$dna_filename\"\n"; die; } @DNA = ; close DNAFILE; $DNA = join( '', @...++$errors; } } print "Adenine = $count_of_A\n"; print "Cytosine = $count_of_C\n"; print "...2908 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...2908 days ago
- ...rser; # Use DAS of UCSC to fetch specific sequence by its given chromosome position # From here: https://ww...if (! $size) { die "ERROR: You must pass three arguments: chr. num., position, and size.\n$usage";...
2902 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";2906 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2906 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2906 days ago
- ...# match pattern in dna2 $m2 = $dna2 =~ m/$pattern/g; print “Was the ATG pattern found in dna2 : $m2 \n”; # find the position of the pattern match in dna1 $pos = index($dna1, $pattern);...
2901 days ago
