blast-wrapper
blast-wrapper is a node.js web-service wrapper for fetching pairwise BLAST or BLAST+ alignments against a fixed reference.
In theory this should be faster than a CGI wrapper.
I use this for aligning sequences to the mitochondrial genome.
A mitochondrial BLAST index and sample config files are provided.
Usage
From github:
git clone git@github.com:leipzig/blast-wrapper.git
cd blast-wrapper
npm start
From npm:
npm install blast-wrapper
npm blast-wrapper start
To access:
http://localhost:8080/?name=mysequence&seq=TGGTCAACCTCGACCTAGGCCTCCTATTTATTCTAGCCACCG
Result:
BLASTN 2.2.28+
Query= mysequence
Length=42
Subject= gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete
genome
Length=16569
Score = 70.4 bits (35), Expect = 4e-16
Identities = 40/41 (98%), Gaps = 0/41 (0%)
Strand=Plus/Plus
Query 1 TGGTCAACCTCGACCTAGGCCTCCTATTTATTCTAGCCACC 41
||||||||||| |||||||||||||||||||||||||||||
Sbjct 3590 TGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACC 3630
Lambda K H
1.39 0.747 1.38
Gapped
Lambda K H
1.39 0.747 1.38
Effective search space used: 546480
Matrix: blastn matrix 1 -5
Gap Penalties: Existence: 5, Extension: 3