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SW:BLAST

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BLAST & BLAST+

GCATemplates available: ada (blastx)

 module spider BLAST

or

 module spider BLAST+

The maximum recommended number of cores to use with blast is 8.

BLAST+ v2.7.1 blastp benchmarks for 1 protein sequence vs nr on Terra

 1 core     2GB mem   36.1 minutes
 7 cores   12GB mem   14.6 minutes
 8 cores   14GB mem   14.2 minutes
28 cores   54GB mem   27.5 minutes

BLAST version 4 databases (pre BLAST+ 2.8.1) such as nr and nt can be found here (BLAST+ uses the same databases):

 /scratch/data/bio/blast  (Terra)
 /scratch/datasets/blast  (Ada)

Sample BLAST+ command:

 blastx -query my_protein_sequences.fasta -db /scratch/datasets/blast/nr -outfmt 10 -out my_protein_sequences_nr_blastout.csv

To see the current version of the nr or nt database, load the latest version of BLAST+ and use the following command:

Terra:
blastdbcmd -info -db /scratch/data/bio/blast/nr

Ada:
blastdbcmd -info -db /scratch/datasets/blast/nr

BLAST+ version 2.8.1 and newer supports the newest version 5 of the BLAST database which allows limiting a search based on taxonomy at the species level.

The version 5 BLAST nr and nt databases are in the following directories. Let us know if you need others.

Terra:
/scratch/data/bio/blastdb_v5/nr_v5
/scratch/data/bio/blastdb_v5/nt_v5

Ada:
/scratch/datasets/blastdbv5/nr_v5
/scratch/datasets/blastdbv5/nt_v5

If your taxid is not recognized, it is most likely too high of a taxon level. Get subtree species taxid list from this webpage (33208 used as an example): https://www.ncbi.nlm.nih.gov/taxonomy/?term=txid33208%5Bsubtree%5D