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Difference between revisions of "SW:BLAST"

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(BLAST & BLAST+)
(BLAST & BLAST+)
Line 8: Line 8:
 
   module spider BLAST+
 
   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
 +
<pre>
 +
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
 +
</pre>
  
 
BLAST version 4 databases (pre BLAST+ 2.8.1) such as nr and nt can be found here (BLAST+ uses the same databases):
 
BLAST version 4 databases (pre BLAST+ 2.8.1) such as nr and nt can be found here (BLAST+ uses the same databases):
   /scratch/datasets/blast
+
   /scratch/datasets/blast (Ada)
 +
  /scratch/data/bio/blast  (Terra)
  
 
Sample BLAST+ command:
 
Sample BLAST+ command:
Line 28: Line 38:
 
</pre>
 
</pre>
  
The version 5 BLAST nr and nt databases are in the following directory. Let us know if you need others.
+
The version 5 BLAST nr and nt databases are in the following directories. Let us know if you need others.
 
<pre>
 
<pre>
 +
Ada:
 
/scratch/datasets/blastdbv5/nr_v5
 
/scratch/datasets/blastdbv5/nr_v5
 +
/scratch/datasets/blastdbv5/nt_v5
  
/scratch/datasets/blastdbv5/nt_v5
+
Terra:
 +
/scratch/data/bio/blastdb_v5/nr_v5
 +
/scratch/data/bio/blastdb_v5/nt_v5
 
</pre>
 
</pre>
  

Revision as of 12:42, 10 February 2020

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

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 use the following command:

module load BLAST/2.2.26-x64-linux
fastacmd -d /scratch/datasets/blast/nr -I

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

module load BLAST+/2.8.1-intel-2017b

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

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

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