Example files of SeqsExtractor

Download Example Files

To download exemples files mentioned in the section bellow open a terminal windows and hit:

SeqsExtractor -d

This will create a folder called example_files, this folder contains a file example_files.tar.gz that contain the following folders:

1. M.musculus_data

1.1 M.musculus_NCBI_entire_genome.fasta

The .FASTA files M.musculus_NCBI_entire_genome.fasta is the complete genome of mouse (Mus musculus) nucleotide sequences, this file can be used as query sequences for the BLASTx/BLASTn search.

Mus_musculus_uniprot_swisprot

Inside M.musculus_data you can see a folder called Mus_musculus_uniprot_swisprot which contain a preformatted BLAST database of all available mouse protein sequences obtained in The universal protein resource (UniProt) by searching for "mouse" in the search field and filtering the search to show only Reviewed sequences (http://www.uniprot.org/uniprot/?query=mouse&fil=reviewed%3Ayes&sort=score). This file can be used as subject database of BLASTx search (-db). We created this database using the following BLAST command:

makeblastdb -in Mus_musculus_uniprot_swisprot.fasta -dbtype prot