Introduction

BLAST finds regions of similarity between biological sequences.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Usage

module load blast/2.2.22

blast data sets

A common data set is maintained on the cluster in the location :

/scratch/support/blast/db

Installation of the dataset:

cd /scratch/support/blast/db/blastdb
wget http://www.ncbi.nlm.nih.gov/BLAST/docs/update_blastdb.pl

 ./update_blastdb.pl --showall
Connected to NCBI
16SMicrobial
cdd_delta
env_nr
env_nt
est
est_human
est_mouse
est_others
gss
htgs
human_genomic
human_genomic_transcript
mouse_genomic_transcript
nr
nt
other_genomic
pataa
patnt
pdbaa
pdbnt
refseq_genomic
refseq_protein
refseq_rna
refseqgene
sts
swissprot
taxdb
tsa_nt
vector
wgs

 perl update_blastdb.pl --passive nr

Installation

mkdir -p /sw/blast/2.2.22/src
cd /sw/blast/2.2.22/src
cp /tmp/blast-2.2.22-x64-linux.tar.gz .
cd /sw/blast/2.2.22/
tar -zxvf src/blast-2.2.22-x64-linux.tar.gz
cd /sw/blast/2.2.22/blast-2.2.22
mv * ../
cd /sw/blast/2.2.22/
rmdir blast-2.2.22

>>>>>>>>>>>>>>>>>>>>>
See installation for ncbi on separate confluence page
Blast programs find dot.ncbirc through the environment variable, NCBI.
The dot.ncbirc file may be copied and modified; see BLAST documentation.
Placed this in /sw/blast/2.2.22/local

 cat dot.ncbirc
[NCBI]
Data=/sw/blast/2.2.22

[BLAST]
BLASTDB=/sw/blast/db
BLASTMAT=/sw/blast/2.2.22


>>>>>>>>>>>>>>>>>>>>>>

cd /sw/blast/2.2.22
ln -s /sw/bioinformatics/ncbi/2009.3 ncbi

Reference

1. http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome
2. http://bioinformatica.info/component/content/article/35-software/122-blast-2222-now-available
3. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/
4. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/blast-2.2.22-ia64-linux.tar.gz
5. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/ncbi.tar.gz
6. http://biskit.pasteur.fr/install/applications/local-blast