Diamond

This is very fast alternative to the blastx program. This page contains some details about the program

key points made

• Describes blastx as the "gold standard"
• highest value placed on sensitivity

Running in gridengine

Here's a workable script

#!/bin/bash 
#$ -cwd 
#$ -j y
#$ -S /bin/bash 
#$ -V
#$ -q single.q
#$ -pe multi 16
module load diamond
diamond blastx -p $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab 
diamond view -a N95.daa -o N95.m8