Results for "sequence"
Bio-Scripts
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...1092 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' =...2906 days ago
- ...l -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs...le $patFile = "/home/anjana/patterns/polyA.pat"; # Go to sequence directory and open it (i.e, r...
2906 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA =...
2907 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...2907 days ago
- ...my $RNA = $DNA; $RNA =~ s/T/U/g; print "RNA sequence is $RNA\n"; #find the reve...g substitution operator #first - reverse the sequence my $rcDNA = reverse($DNA);...ng translation operator #first - reverse the sequence $rcDNA = reverse($DNA); #th...
2907 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...2907 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...2906 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...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 $in_fh, '', $ou...2905 days ago
