BLAST ( Basic local alignment search tool ).

 What is BLAST ..........? 

Blast is a ( basic local alignment search tool ) commonly used for sequences database search program based on sequences similarity .

(http://blast.ncbi.nlm.nih.gov/Blast.

The BLAST program was developed by Stephen Altschul of NCBI in 1990 and has since  become one of the most popular program for sequences analysis .

- the objective is to find high scoring ungapped segments among related sequences.

Programs of BLAST :- 

1) Nucleotide -nucleotide BLAST ( blast n ) :-

This program given a DNA query, returns the most similar DNA sequences from the DNA database that the user specifies .

2) Protein - protein BLAST (blast p ) 

This program gives a protein query , return the most similar protein sequences from the protein database that the user specific .

3) Nucleotide 6- frame translation ( blast x)

This program compares the six frame conceptual translation product of nucleotide query sequence (both strand ) against the protein sequences database.

4) Nucleotide 6-frame translation nucleotide 6- frame translation ( t blast x)

this program is the slowest of the blast family . It translates the query nucleotide sequence in all six possible frame and compares it against the six frame translation of a nucleotide sequences database . the purpose of tblastx is to find very distant relationships between nucleotide sequences.

5) Protein - nucleotide 6- frame translation (tblastn)

This program compares a protein query against the all six reading frames of a nucleotide sequence database.

6) Position -specific iterative BLAST (PSI-BLAST ) ( blastpgp)

This program is used to find distant relatives of a protein . Frist, a list of all closely related protein is created . This proteins are combined into a general profile sequences which summarises significant features present in this sequences .

A query against the protein database is then run using this profiles and larger group of protein is found .This larger group is used to construct another profiles .

It is more sensitive in picking up evolutionary relationship than a standard protein- protein BLAST .

Use of BLAST :-

BLAST can be used for several purpose . These include identifying species , locating domains , establishing phylogeny , DNA mapping , and comparison . 

1) Identifying species :- 

With the use of BLAST , you can possibly correctly identify a species or find homologous species . This can be useful ,eg . When you are working with a DNA sequence from a unknown species .

2) Locating domains :- 

When working with a protein sequence you can input it into BLAST , to locate known domains within the sequence of interest .

3) Establishing phylogeny :-

Using the result received through BLAST you can create a phylogenetic trees using the BLAST web page.

4) DNA mapping :- 

When working with the new species , and looking to sequences a gene at an unknown location , BLAST can compare the chromosomal position of the sequences of interest to relevant sequences in the database .

5) Comparison:- 

When working with gene , BLAST can locate common gene in two related species .and can be used to map annotations from one organism to another .