This script uses the NCBI taxonomy database to classify and separate sequences from a given a list of FASTA formatted sequences.
Any rank parameter from NCBI taxonomy database can be use to filter the desirable sequences.

To use it simply save it as perl script and call:

LINUX:> builddb.pl input.file format

BuildDB accepts all formats included on Bioperl

You should customize the following part of the script to fit on your needs.

 

if (($node->rank eq "superkingdom") && ($node->scientific_name eq "Bacteria"))
{
#print $node->rank,"\t", $node->scientific_name, "\n";
# grava no texto
$seq_out->write_seq($seq);
###Put it on an array for counting purposes
push(@in, $node->scientific_name);

 

[code]if (($node->rank eq "superkingdom") && ($node->scientific_name eq "Bacteria"))
{
#print $node->rank,"\t", $node->scientific_name, "\n";
# grava no texto
$seq_out->write_seq($seq);
###Put it on an array for counting purposes
push(@in, $node->scientific_name);
[/code]