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BLAST Analysis and Algorythim

The document discusses BLAST and FASTA algorithms for comparing biological sequences like DNA and proteins. BLAST uses local rather than global alignment to detect similar regions between sequences that may only share isolated similarities. It performs heuristic searches to efficiently compare a query sequence against a database and identify statistically significant matches above a certain threshold. Dynamic programming is used to solve subproblems and combine their solutions for optimization problems like sequence alignment. The Smith-Waterman algorithm specifically performs local sequence alignment to find similar regions between two sequences.

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Salman Shafiq
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157 views11 pages

BLAST Analysis and Algorythim

The document discusses BLAST and FASTA algorithms for comparing biological sequences like DNA and proteins. BLAST uses local rather than global alignment to detect similar regions between sequences that may only share isolated similarities. It performs heuristic searches to efficiently compare a query sequence against a database and identify statistically significant matches above a certain threshold. Dynamic programming is used to solve subproblems and combine their solutions for optimization problems like sequence alignment. The Smith-Waterman algorithm specifically performs local sequence alignment to find similar regions between two sequences.

Uploaded by

Salman Shafiq
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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BLAST and FastA

Dr. Muhammad Tahir


Department of Environmental Sciences
CIIT Vehari
What is BLAST
BLAST for Basic Local Alignment Search Tool is an
algorithm for comparing primary biological sequence
information, such as the amino-acid sequences of
different proteins or the nucleotides of DNA
sequences.

A BLAST search enables a researcher to compare a


query sequence with a library or database of
sequences, and identify library sequences that
resemble the query sequence above a certain
threshold.
 Instead of relying on global alignments (commonly
seen in multiple sequence alignment programs)
BLAST emphasizes regions of local alignment to
detect relationships among sequences which share
only isolated regions of similarity.
Database Homology
Searching
Use algorithms to increase efficiency and provide a

mathematical basis for searching which can be translated into

statistical significance

 Assumes that sequence, structure and function are interrelated.

 These are experiential methods approximating Smith Waterman


What is a Heuristic (experimental)
Method?
 Many problems in Artificial Intelligence are
optimization problems.

 An approximation (or heuristic) search


method does not mean that the search
algorithm will find a wrong solution.

 If a solution is found, that solution is


guaranteed to be valid, but it may not be best
possible.
Statistical Significance of
Sequence Comparisons
• Assess the statistical significance of a particular global
alignment by generating many random sequence pairs
of the appropriate length and composition, and
calculating the optimal alignment score for each.
BLAST
Statistics
 A local alignment without gaps consists simply
of a pair of equal length segments, one from
each of the two sequences being compared.

 These are called high-scoring segment pairs or


HSPs.

 BLOSUM 62 is the default matrix in BLAST


2.0.
• You can select a different matrix for your Blast
search.
• Though it is customized for comparisons of
moderately distant proteins, it performs well in
detecting closer relationships.
Dynamic Programming
In mathematics, Computer Science, Economics, and Bioinformatics,
Dynamic Programming is a method for solving complex problems by
breaking them down into simpler sub-problems.
The idea behind dynamic programming is quite simple. In general, to solve
a given problem, we need to solve different parts of the problem (sub-
problems), then combine the solutions of the sub-problems to reach an
overall solution.
Dynamic programming algorithms are used for optimization (for example,
finding the shortest path between two points, or the fastest way to multiply
many matrices)
The Smith–Waterman algorithm performs local sequence alignment;
that is, for determining similar regions between two DNA or protein
sequences.
Instead of looking at the total sequence, the Smith–Waterman algorithm
compares segments of all possible lengths and optimizes the similarity
measure.
The algorithm was first proposed by Temple F. Smith and Michael S.
Waterman in 1981.
 Smith–Waterman is a dynamic programming algorithm. It has the
desirable property that it is guaranteed to find the optimal local alignment
with respect to the scoring system being used.
Procedure
To obtain the optimum local alignment, start
with the highest value in the matrix. Then, go
backwards to one of positions, and
depending on the direction of movement
used to construct the matrix. This
methodology is maintained until a matrix cell
with zero value is reached.
For the example, the results are:
Sequence 1 = A-CACACTA
Sequence 2 = AGCACAC-A
The Smith–Waterman algorithm

Sequence 1 = A-CACACTA
Sequence 2 = AGCACAC-A

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