R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org...1106 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' =...2920 days ago
2920 days ago
2921 days ago
Count the frequency of base G in a given DNA sequence
...and $currentPos my $countG = 0; my $currentPos = 0; #calculate the length of $DNA my $DNAlength = length($DNA); #for each letter in the sequence check if it is the base G #i...2921 days ago
2921 days ago
Parse a genbank file using regular expressions
..."Locus: $2\n"; } elsif (/(VERSION.*GI:)(\d*)/) { print "GI: $2\n"; } elsif (/(DEFINITION\s*)(.*)(\.)/) { print "Sequence name: $2\n"; } elsif...2921 days ago
Perl script to Mutate a DNA Sequence
...-w # This script randomly mutates the DNA sequence and generates 10 successive m...s script it asks for the file name of the DNA sequence. # If the DNA sequence file...ws: c:\rnafile.txt # In Linux : /home/user/sequence/rnafile.txt use File::Path...2920 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
...While executing this script it asks for the file name of the DNA sequence. If the sequence file is not available in the...the path. In windows: c:\dnafile.txt, In Linux: /home/user/sequence/dnafile.txt print "ENTER T...2920 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 $in_fh, '', $ou...2919 days ago