Previously, I shared a PERL script to perform batch BLAST to the NCBI server. This PERL script uses Bioperl modules so make sure that bioperl is installed on your machine. This PERL script is written by Dr. Paul Stothard, University of Alberta. It will perform BLAST in more coustomizable way. You can enter your own parameters easily and BLAST result will be pre-parsed. So you don't any NCBI BLAST parser for your BLAST results. As usual don't forget to drop a comments.

Script name	Download
NCBI-blast.pl

Necessary parameterS

 -i - Input file containing multiple fasta sequences. [File].
 
 -o - Output file to create. [File].
 
 -d - Database to search. [File].
 
 -b - BLAST program (blastn, blastp, blastx, tblastn, tblastx). [String].

Optional parameterS

 -e - Entrez query to limit results. [String].
 
 -h - Number of hsps to keep. [Integer]. Default is to keep all hsps.
 
 -l - Whether to filter the query sequence. [F/L/R/LR]. Default is
 F. Acceptable values are 'F' for no filter, 'L' for low complexity,
 'R' for human repeats, or 'LR' for both.
 
 -a - Minimum alignment length to keep. [Integer]. Default is to keep  all alignments. 
 
 -p - Minimum alignment length to keep, expressed as a proportion of
 the query sequence length. [Real]. Overrides -a. Default is to keep
 all alignments.
 
 -s - Minimum alignment score to keep. [Integer]. Default is to keep
 all alignments.
 
 -n - Minimum alignment identity to keep. [Real]. Default is to keep
 all alignments.
 
 -x - Expect value to supply to the BLAST program. [Real]. Default is
 10.0.
 
 -t - Number of hits to keep. [Integer]. Default is 5.
 
 -f - Whether to fetch sequence descriptions using Entrez. [T/F].
 Default is T.
 
 -Q - The genetic code to use for translated BLAST searches. [Integer].
 Default is 1.
 
 -accession - Whether to attempt to replace the hit ID (the gi number)
 with an accession number. Requires that "-f" be set to
 "T". [T/F]. Default is T.

Dependencies

use Getopt::Long;
use LWP::UserAgent;
use HTTP::Request::Common;