How to Extract Entries From Multiple Fasta

FASTA formats represent nucleotide sequences.

FASTA is a text-based format used in bioinformatics for representing sequences, especially those of nucleotides and peptides, with base pairs represented by a single letter. A FASTA sequence consists of a single-line description, distinguished by a “greater than” symbol on the first line, followed by a multi-line nucleotide or peptide sequence. You can extract multiple sequences from a FASTA file using special modules, or add-ons, to the Perl programming language, known as BioPerl, that have been specially developed to handle the FASTA format. You can also manually code a Perl script to match patterns in a file or use other available tools to extract FASTA sequences.

Instructions

Things You'll Need

• FASTA file
• Perl editor
• BioPerl
• ActiveState Perl
• Biopieces

1. • 1
     Launch your Perl editor application. You may use a simple text editor, such as Notepad. You will need to save the file with a “.pl” extension to indicate that it is a Perl program.
   • 2
     Extract a sequence from a multiple-FASTA file by performing pattern-matching in Perl, by typing the following code into the editor:

     #!/usr/bin/perl
     my $ fasta_seq = shift;
     my $sequence = shift;
     my $workfile = `cat $ fasta_seq `;
     my ($fasta_seq) = $workfile =~ /(>$sequence[^>]+)/s;
     print $fasta_seq;
   • 3
     Extract the sequences from the FASTA file using BioPerl. You can extract multiple sequences by typing the following code into the editor:

     #!/bin/perl -w

     use Bio::SeqIO;

     $sequenceobject = Bio::SeqIO->new(-file => "fasta_file_path", -format => "fasta" );

     The Bio::SeqIO module provides seamless sequence processing. You can retrieve a single sequence using the following statement:

     $retrievedsequence = $ sequenceobject ->next_seq;

     You can loop through the object and retrieve multiple sequences, as follows:

     while ($retrievedsequence = $ sequenceobject ->next_seq)
     {
     print $ retrievedsequence ->seq,"\n";
     }
   • 4
     Extract the sequences from the FASTA file using the “Biopieces” application, which is framework containing a set of modular tools for manipulating bioinformatics data. You run your Biopieces command at the command line.

     read_fasta -i fasta_file | grab -p sequence | write_fasta -o sequence_file –x

     This is a good option if you are not very technically inclined, as the framework encapsulates much of the programming effort required to process the FASTA file and output the matched sequences.