Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation conda install -c bioconda blast #Windows installation First: Download ftp://ftp.ncbi.nlm.nih.gov/blast/executa...1145 days ago
2915 days ago
Count the frequency of base G in a given DNA sequence
...my $DNA = "GATTACACAT"; #initialize $countG and $currentPos my $countG = 0; my $curr...e check if it is the base G #if 'yes' increment $countG while($currentPos <...nt out the number of Gs print "There are $countG G bases\n";2915 days ago
2915 days ago
Read lines from input file – print lines that match a regular expression
...e; #read the line-by-line for each line ask if it matches the regex print it if it matches while($li...e; if ($line =~ /^ATG?C*[ATCG]+?A{3,10}$/) { print "$line\n"; } } e...2915 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";2915 days ago
Parse a genbank file using regular expressions
...{ if (/(LOCUS\s*)(\w*)(.*)/) { print "Locus: $2\n"; } elsif (/(VERSION.*GI:)(\d*)/) { print "GI: $2\n"; } elsif...$cds_start = $2; $cds_end = $4; print "CDS: $cds_start - $cds_end\n...2915 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
...= Bio::SeqIO->newFh('-file' => "$inFile" , '-format' => 'Fasta'); $out = Bio::SeqIO->newFh('-format' => 'Genbank'); print $out $_ while ;2914 days ago
2914 days ago
Perl script to Mutate a DNA Sequence
...the same directory of this script, enter the file name with its full...nafile.txt use File::Path; print "ENTER THE FILENAME OF THE DN...utant; $mutant = mutate($DNA); print "Mutate DNA\n\n"; print "H..., 'G', 'T'); return randomelement(@nucleotides); }2914 days ago