Information on BLAST


What is BLAST?
BLAST stands for Basic Local Alignment Search Tool; it provides a method for rapid searching of nucleotide and protein databases.Since the BLAST algorithm detects local as well as global alignments, regions of similarity embedded in otherwise unrelated proteins can be detected. Both types of similarity may provide important clues to the function of uncharacterized proteins.

Blast Family of Programs
The BLAST family of programs allows all combinations of DNA or protein query sequences with searches against DNA or protein databases:

A simpler view:

                                  Protein Level Comparison

   

DATABASE

   

DNA

Protein

QUERY

DNA

tblastx

blastx

Protein

tblastn

blastp



                                  DNA Level Comparison

   

DATABASE

   

DNA

Protein

QUERY

DNA

blastn

N/A

Protein

N/A

N/A

 

TYPES OF BLASTS
1. BLAST score-based single-linkage clustering - (BLASTCLUST )

2. STAND-ALONE BLAST
Stand-Alone BLAST is for users who wishes to run at their own institution. One reason to do so might be the wish to use private databases.

3. BLASTALL
Blastall may be used to perform all five flavors of blast comparison. One may obtain the blastall options by executing 'blastall -' (note the dash). A typical blastall to perform a blastn search (nucl. vs. nucl.) of a file called QUERY would be:
blastall -p blastn -d nr -i QUERY -o out.QUERY
The output is placed into the output file out.QUERY and the search is performed against the 'nr' database. If a protein vs. protein search is desired, then 'blastn' should be replaced with 'blastp' etc.

4. MEGABLAST
MegaBlast implements a greedy algorithm for the DNA sequence gapped alignment search. Since MegaBlast can only work with DNA sequences, the only program it supports is Blastn. Unlike BLAST, MegaBlast is most efficient in both speed and memory requirements with non-affine gap penalties. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". It is up to 10 times faster than more common sequence similarity programs and therefore can be used to swiftly compare two large sets of sequences against each other.

5. Reversed Position Specific Blast - (RPS-BLAST )
RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles. This is the opposite of PSI-BLAST that searches a profile against a database of sequences, hence the 'Reverse'. RPS-BLAST uses a BLAST-like algorithm, finding single- or double-word hits and then performing an ungapped extension on these candidate matches. If a sufficiently high-scoring ungapped alignment is produced, a gapped extension is performed and those (gapped) alignments with sufficiently low expect value are reported. This procedure is in contrast to IMPALA that performs a Smith-Waterman calculation between the query and each profile, rather than using a word-hit approach to identify matches that should be extended.

RPS-BLAST uses a BLAST database, but also has some other files that contain a precomputed lookup table for the profiles to allow the search to proceed faster. Unfortunately it was not possible to make this lookup table architecture independent (like the BLAST databases themselves) and one cannot take a RPS-BLAST databases prepared on a big-endian system (e.g., Solaris Sparc) and run it on a small-endian system (e.g., NT).

Links: BLAST: Further Information -A simple explanation on individual iprograms


Comments and suggestions to:Professor Bharat Patel <b.patel@griffith.edu.au>
HTML'd by Bharat Patel
[Created: 11 February 2008]
[Updated: 24 February 2008]