Running BLAST optimally

This is a brief description of a couple of experiments that I (mjv08) have tried out using blast in order to determine the best way in which to run it.

Okay, so you have a fasta file you wish to blast. The file I had was supplied by Russ (rom) and contained 18788 sequences in a fasta file. He wanted to run the default settings for blast using blast2go. These settings using blast+ on the command line are;

blastx -db nr -query input.fasta -out output.xml -evalue 1e-3 -outfmt 5 -show_gis -num_threads 1

The first thing I have done is to take a single sequence,