variants of blast

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VARIANTS OF BLAST VARIANTS OF BLAST

By- Darshana D Ghadi

Roll No. - 03



BLAST

The Basic Local Alignment Search Tool (BLAST) isa computer program for finding regions of localsimilarity between two DNA or protein sequences.

The BLAST programs have been designed forspeed, with a minimal sacrifice of sensitivity todistant sequence relationships.



ADVANCED

BLAST METHODS

The NCBI BLAST pages have several advancedBLAST methods available

y PSI-BLAST

y PHI-BLAST

y Mega-BLAST

All are powerful methods based on proteinsimilarities



POSITION-SPECIFIC-ITERATED-BLAST PSI-BLAST

Position-Specific Iterative (PSI) BLAST is a programbased on the BLAST algorithm.

The added sensitivity of this program over regularBLAST comes from the use of a (PSSM) or profilethat is constructed (automatically) from a multiplealignment of the highest scoring hits in the initialBLAST search.

The profile is then used to perform additional BLAST searches (called iterations) and the results of eachiteration used to refine the profile.

Fast & simple to use.



PSI-BLAST PRINCIPLE

A PSI-BLAST query is identical to a BLAST querywith added specification by the use of theexpectation (E) value better (lower) than the

inclusion threshold (0.005 by default) for inclusionof a match in the first iteration.

The user can continue to search iteratively until

satisfied that no new matches will be identified.

The point at which no new hits are identified byadditional searches is known as "convergence".



Step 1 : Input the data and enter the Choose the database to search.



Step 2. Set program options or choose defaults.



Step 3. Set the output formatting options and perform the search.



Step4. PSI-BLAST Output



Detailed output of PSI-BLAST



PATTERN HIT INITIATED ² BLAST PHI-BLAST

PHI-BLAST expects as input a protein querysequence and a pattern contained in that sequence.

PHI-BLAST searches the specified database forother protein sequences that also contain the inputpattern and have significant similarity to the querysequence in the vicinity of the patternoccurrences.

Limitations of PHI-BLAST

PHI-BLAST can be used only for protein²protein

comparison.



MEGABLAST

MEGABLAST is specifically designed to efficientlyfind long alignments between very similarsequences.

In addition to the expect value significance,MEGABLAST also provides an adjustable percentidentity cut-off that overrides the significancethreshold.

Mega BLAST is also able to efficiently handle muchlonger DNA sequences than the blastn program oftraditional BLAST algorithm.



MEGABLAST search like a Basic BLAST search,but allows you to change certain parameters inorder to perform a more specified BLAST search:

. specify an organism or taxonomic class for yoursearch

. set the E value

. filter for low complexity or human repeats

. query Genetic Codes (blastx and tblastx only)

. change your scoring matrix (BLOSUM62 is thedefault scoring matrix)



There are particular values for different parametersthat needs to be set for Mega BLAST in order to have

the best possible results are stated below:

Word Size - Mega BLAST is most efficient with wordsizes 16and larger, although word size as low as 8 canbe used.

Percent Identity - If this parameter P is set, only thealignments with identity percentage higher than P will beretained.

Gapping Parameter - The non-affine version of MegaBLAST requires significantly less memory and is alsosignificantly faster, however affine gapping parameterscan also be used, preferably with larger word sizes.



REFERENCES

Analys is of Bas ic Local Al ignmen ts In Biomolec ular Seq uences . A thes is by - Rajn i K an t J ayaswal

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