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Variants of Blast: By-Darshana D Ghadi Roll No. - 03

There are several variants of the BLAST algorithm available on the NCBI BLAST pages, including PSI-BLAST, PHI-BLAST, and Mega-BLAST. PSI-BLAST improves on regular BLAST by using profiles generated from an initial search to refine subsequent searches. PHI-BLAST searches for protein sequences that contain the same patterns as the query. Mega-BLAST is optimized for finding long alignments between very similar DNA sequences and allows users to customize parameters like percent identity and word size.

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179 views17 pages

Variants of Blast: By-Darshana D Ghadi Roll No. - 03

There are several variants of the BLAST algorithm available on the NCBI BLAST pages, including PSI-BLAST, PHI-BLAST, and Mega-BLAST. PSI-BLAST improves on regular BLAST by using profiles generated from an initial search to refine subsequent searches. PHI-BLAST searches for protein sequences that contain the same patterns as the query. Mega-BLAST is optimized for finding long alignments between very similar DNA sequences and allows users to customize parameters like percent identity and word size.

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darshana_707
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VARIANTS OF BLAST

By- Darshana D Ghadi


Roll No. - 03
BLAST

 The Basic Local Alignment Search Tool (BLAST) is


a computer program for finding regions of local
similarity between two DNA or protein sequences.

 The BLAST programs have been designed for


speed, with a minimal sacrifice of sensitivity to
distant sequence relationships.
ADVANCED BLAST METHODS

The NCBI BLAST pages have several advanced


BLAST methods available
 PSI-BLAST
 PHI-BLAST
 Mega-BLAST

All are powerful methods based on protein


similarities
POSITION-SPECIFIC-ITERATED-BLAST
PSI-BLAST

 Position-Specific Iterative (PSI) BLAST is a program


based on the BLAST algorithm.

 The added sensitivity of this program over regular


BLAST comes from the use of a (PSSM) or profile that
is constructed (automatically) from a multiple alignment
of the highest scoring hits in the initial BLAST search.

 The profile is then used to perform additional BLAST


searches (called iterations) and the results of each
iteration used to refine the profile.

 Fast & simple to use.


PSI-BLAST PRINCIPLE

 A PSI-BLAST query is identical to a BLAST query


with added specification by the use of the
expectation (E) value better (lower) than the
inclusion threshold (0.005 by default) for inclusion
of 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 by


additional 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 – BLAST
PHI-BLAST

 PHI-BLAST expects as input a protein query


sequence and a pattern contained in that sequence.

 PHI-BLAST searches the specified database for


other protein sequences that also contain the input
pattern and have significant similarity to the query
sequence in the vicinity of the pattern
occurrences.

 Limitations of PHI-BLAST
PHI-BLAST can be used only for protein–protein

comparison.
MEGABLAST

 MEGABLAST is specifically designed to efficiently


find long alignments between very similar
sequences.

 In addition to the expect value significance,


MEGABLAST also provides an adjustable percent
identity cut-off that overrides the significance
threshold.

 Mega BLAST is also able to efficiently handle much


longer DNA sequences than the blastn program of
traditional BLAST algorithm.
 MEGABLAST search like a Basic BLAST search,
but allows you to change certain parameters in
order to perform a more specified BLAST search:

. specify an organism or taxonomic class for your


search

. set the E value

. filter for low complexity or human repeats

. query Genetic Codes (blastx and tblastx only)

. change your scoring matrix (BLOSUM62 is the


default scoring matrix)
There are particular values for different parameters
that 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 word


sizes 16and larger, although word size as low as 8 can
be used.

 Percent Identity - If this parameter P is set, only the


alignments with identity percentage higher than P will
be retained.

 Gapping Parameter - The non-affine version of Mega


BLAST requires significantly less memory and is also
significantly faster, however affine gapping parameters
can also be used, preferably with larger word sizes.
REFERENCES

 http://www.google.com

 Analysis of Basic Local Alignments In Biomolecular


Sequences. A thesis by- Rajni Kant Jayaswal
THANK
YOU

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