BASIC LOCAL ALIGNMENT SEARCH TOOL ( BLAST)

AIM

       To study the BLAST similarity search Tool.

INTRODUCTION

        The Blast tool finds regions of local similarity between sequences. The program compares nucleotide (or) protein sequences to sequence Data base and calculates the statistical significance of matches. Blast can be used to infer functional and evolutionary relationships between sequences and also helps to identify members of gene families.

TYPES OF BLAST SEARCH

NUCLETIDE DATABASES

(1) MegaBLAST

          It quickly searches for highly similar sequences with large queries.

(2) Discontiguous MegaBLAST

          It quickly search for divergent sequences.

(3) BLAST n

          It is a nucleotide-nucleotide BLAST which searches for short and nearly exact matches.

PROTEIN

(1) BLAST p

          It is a protein-protein BLAST which searches for exact matches.

(2) PSI-BLAST

          Position specific Iterated BLAST

(3) PHI-BLAST

          Pattern Hit Initiative BLAST

TRANSLATED BLAST

(1) BLAST x

          Translated DNA query with protein Database

(2) tBLASTn

           Compares protein query with translated DNA Database.

(3) tBLASTx

            Compares translated DNA query with translated DNA database.

Specialised BLAST Program

(1) Geo BLAST

            It searches for gene expression Data.

(2) bl2seq

            Aligns two sequences.

(3) Ig BLAST

            It is an immunoglobin protein.

  

EXPECTATION VALUE

            The expectation value (E) is a parameter that describes the number of Hits one can expect to see just by chance. When searching a Database of a particular size. It decreases exponentially with the score (S) that is assigned to a match between two sequences essentially the e value describes the random Back ground noise that exists for matches between sequences.

For  example : An  E value of one assigned to a hit can be interpreted as meaning that the Database of current size one might expect to see one match. With a similar sore simply by chance. This means that lower the E value (or) the closer it is to zero then it is a significant match.

ALGORITHM

(1) Go to NCBI Homepage and click BLAST.

(2) Then select the type of BLAST search you want.

(3) Obtain the FASTA format of the given query.

(4) After that paste your sequence in BLAST program.

(5) Select the appropriate parameters (if any).

(6) Click Format (or) BLAST to perform search operation.

(7) You will get results displayed based on the E value and score.

(8) Interpretation of results to get significant matches

  

QUERY SEQUENCE

>gi|205943662|gb|ACI04728.1| lysin [Haliotis sorenseni]

EVALKVQIIAGFDRTLVKWLRTHGGTLSHVQKKALYFVNRRYMQTH