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(BLAST & BLAST+)
(BLAST & BLAST+)
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BLAST+ version 2.8.1 supports the newest version 5 of the BLAST database which allows limiting a search based on taxonomy.
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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.
  
 
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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):
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https://www.ncbi.nlm.nih.gov/taxonomy/?term=txid33208%5Bsubtree%5D
 
[[ Category:SW ]] [[ Category: Bioinformatics ]]
 
[[ Category:SW ]] [[ Category: Bioinformatics ]]

Revision as of 08:51, 27 March 2019

BLAST & BLAST+

GCATemplates available: ada (blastx)

 module spider BLAST

or

 module spider BLAST+


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

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 directory. Let us know if you need others.

/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