Index of /examples/bioinformatics/blast+

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] refseq_rna.00.nhr 08-Mar-2015 16:03 395M [   ] refseq_rna.00.nin 08-Mar-2015 16:03 29M [   ] refseq_rna.00.nnd 08-Mar-2015 16:03 20M [   ] refseq_rna.00.nni 08-Mar-2015 16:03 79K [   ] refseq_rna.00.nsq 08-Mar-2015 16:03 954M [   ] refseq_rna.00.nog 08-Mar-2015 16:03 9.7M [   ] refseq_rna.00.nsd 08-Mar-2015 16:03 104M [   ] refseq_rna.00.nsi 08-Mar-2015 16:03 2.2M [   ] refseq_rna.nal 08-Mar-2015 16:10 180 [   ] test_query.fa 08-Mar-2015 23:55 2.8K [   ] blast_job.qsub 24-Mar-2015 12:48 467

BLAST+ package example

To run BLAST+ at the command line:

scc4% module load blast+/2.2.30

scc4% blastn -help

scc4% blastdbcmd -db refseq_rna.00 -entry nm_000122 -out test_query.fa


scc4% blastn -query test_query.fa -db refseq_rna.00 -task blastn -dust no -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 2
# BLASTN 2.2.30+
# Query: gi|4557562|ref|NM_000122.1| Homo sapiens excision repair cross-complementation group 3 (ERCC3), transcript variant 1, mRNA
# Database: refseq_rna.00
# Fields: query id, subject id, evalue, bit score
# 2 hits found
gi|4557562|ref|NM_000122.1| gi|4557562|ref|NM_000122.1| 0.0 4962
gi|4557562|ref|NM_000122.1| gi|197101764|ref|NM_001132325.1| 0.0 4569
# BLAST processed 1 queries



To submit a job, execute command:
scc4% qsub -P my_project blast_job.qsub

Manual for BLAST+:
http://www.ncbi.nlm.nih.gov/books/NBK52638/