Install BLAST in Ubuntu/Linux and Window !
...st: Download ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe with your web brow...e defaults, it should put BLAST under C:\Program Files\NCBI\blast-2.7.1+1110 days ago
Count the frequency of base G in a given DNA sequence
...letter in the sequence check if it is the base G #if 'yes' increment $countG while($currentPos < $DNAlength){ my $base = substr($DNA,$currentPos,1); if($base eq "G"){ $cou...2880 days ago
Read lines from input file – print lines that match a regular expression
...for each line ask if it matches the regex print it if it matches while($line = ){ chomp $line; if ($line =~ /^ATG?C*[ATCG]+?A{3,10}$/) { print...2880 days ago
Parse a genbank file using regular expressions
...ading: $!"; # Flag for multiline translation; 1 means translation "in progres...)(\.\.)(\d*)/) { # ex: CDS 357..1541 $cds_start = $2;...lation: "; $protein = $2; $trans = 1; } elsif ($trans) {...2880 days ago
Perl script to Mutate a DNA Sequence
...randomly mutates the DNA sequence and generates 10 successive mutation results....print "Mutate DNA\n\n"; print "HERE ARE THE 10 SUCCESSIVE MUTATIONS:\n\n";...my $current_base = substr($dna, $position, 1); my $newbase;...2879 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...turnType} ) ) ) { print_usage(); exit(1); } $param{returnType} =...ch.fcgi?db=$param{database}" . "&retmax=1&usehistory=y&term=$param{quer...ading records " . ( $retstart + 1 ) . " to " ....2879 days ago
A multilayer perceptron (MLP) neural network in Perl
...############ #Tanh hidden neurons #Linear output neuron #To include an input bias create an #extra input in the training data #and set to 1 ################ User se...2879 days ago
Extract a random sequence from a file
...tput.txt'; open my $in_fh, '', $outputfile; my $size = 21; my $count = 10; while (my $line = ) {...next unless @start_points >= $count; print substr($genome, $_, 21), "\n" for @start_points[0 .....2878 days ago
2873 days ago
Blast result parser with Perl and Bioperl
...T $hsp->start('hit') . "\t" . $hsp->end('hit') . "\t"; # get the similarity value printf OUT "%.1f" , ($hsp->frac_conserved * 100); print OUT "%\t";...2877 days ago