Results for "r"
Bio-Scripts
Install BLAST in Ubuntu/Linux and Window !
...ll -c bioconda blast #Windows installation First: Download ftp://ftp.ncbi.n...blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe with your web browser. #If that FTP...les/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe #Run this installer using the...1160 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA = $DNA.$...difiedDNA and #print out the value of the variable and its length my $DNAl...
2930 days ago
Count the frequency of base G in a given DNA sequence
#!/usr/bin/perl use strict; use warnings; my $DNA = "GAT...ACAT"; #initialize $countG and $currentPos my $countG = 0; my $...my $DNAlength = length($DNA); #for each letter in the sequence c...length){ my $base = substr($DNA,$currentPos,1); if($base eq "G")...2930 days ago
- #!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #transcribe DNA to RNA - T changes to U my $RNA = $DNA; $RNA =~ s/T/U/g; print "RNA seque...substitution operator #first - reverse the sequence my $rcDNA...nt of $DNA using translation operator #first - reverse the seq...
2930 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matches the regex print it if it matches while($line = ){...e =~ /^ATG?C*[ATCG]+?A{3,10}$/) { print "$line\n"; } }...2930 days ago
Check if your coputer ready to use BioPerl
#!/usr/bin/perl use strict; use warnings; #bioperl example code use strict; use warnings; #make the bioperl module (class) accessible to your program use Bio::Seq; print"ok - ready to use Bio::Seq";2930 days ago
Parse a genbank file using regular expressions
...bank) || die "cannot open $gb_report for reading: $!"; # Flag for multiline translation; 1 mean...$2\n"; } elsif (/(VERSION.*GI:)(\d*)/) { pr...357..1541 $cds_start = $2; $cds_end = $4;...Problems: end of translation product not found.\n"; }...2930 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; $inFile = "BRCA2.fa";...ewFh('-file' => "$inFile" , '-format' => 'Fasta'); $out = Bio:...2929 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $m...t directory (relative to $myDir or full path) $outputDir = "...# s/old/new/; #User can process these files as pe...
2929 days ago
Perl script to Mutate a DNA Sequence
#!/usr/local/bin/perl -w # This script randomly mutates the DNA sequence and generates 10 successive mutation re...# Example: # In windows: c:\rnafile.txt # In Linux : /hom...t; $mutant = mutate($DNA); print "Mutate DNA\n\n"; print...randomelement { my(@array) = @_; return $array[...2929 days ago
