blast-plus

Description

Basic Local Alignment Search Tool. BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

Versions

• Anvil: 2.12.0

Module

You can load the modules by:

module load blast-plus

BLAST Databases

Local copies of the blast dabase can be found in the directory /anvil/datasets/ncbi/blast/latest. The environment varialbe BLASTDB was also set as /anvil/datasets/ncbi/blast/latest. If users want to use cdd_delta, env_nr, env_nt, nr, nt, pataa, patnt, pdbnt, refseq_protein, refseq_rna, swissprot, or tsa_nt databases, do not need to provide the database path. Instead, just use the format like this -db nr.

Example job

To run bamtools our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -p PartitionName
#SBATCH --job-name=blast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module load blast-plus

blastp -query protein.fasta -db nr -out test_out -num_threads 4