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    FASTA Algorithm

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    Hemant Samadder
    The FASTA algorithm is a heuristic method for string comparison that uses hash coding to break sequences into small "words or K-tuples" to focus the comparison on diagonal areas of similarity. It proceeds in four main steps: [1] identifying regions of similarity between query and search sequences based on consecutive word matches; [2] rescoring the initial regions and selecting best-scoring subregions; [3] optimally joining compatible initial regions to form approximate alignments; and [4] using dynamic programming to further align the highest-scoring sequences within a band centered on the best initial region. This allows FASTA to achieve faster running times than dynamic programming at the cost of some sensitivity.

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    FASTA Algorithm

    Uploaded by

    Hemant Samadder
    138 views15 pages
    The FASTA algorithm is a heuristic method for string comparison that uses hash coding to break sequences into small "words or K-tuples" to focus the comparison on diagonal areas of similarity. It proceeds in four main steps: [1] identifying regions of similarity between query and search sequences based on consecutive word matches; [2] rescoring the initial regions and selecting best-scoring subregions; [3] optimally joining compatible initial regions to form approximate alignments; and [4] using dynamic programming to further align the highest-scoring sequences within a band centered on the best initial region. This allows FASTA to achieve faster running times than dynamic programming at the cost of some sensitivity.

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    FASTA_Algorithm

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    The FASTA algorithm is a heuristic method for string comparison that uses hash coding to break sequences into small "words or K-tuples" to focus the comparison on diagonal areas of similarity. It proceeds in four main steps: [1] identifying regions of similarity between query and search sequences based on consecutive word matches; [2] rescoring the initial regions and selecting best-scoring subregions; [3] optimally joining compatible initial regions to form approximate alignments; and [4] using dynamic programming to further align the highest-scoring sequences within a band centered on the best initial region. This allows FASTA to achieve faster running times than dynamic programming at the cost of some sensitivity.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    138 views15 pages

    FASTA Algorithm

    Uploaded by

    Hemant Samadder
    The FASTA algorithm is a heuristic method for string comparison that uses hash coding to break sequences into small "words or K-tuples" to focus the comparison on diagonal areas of similarity. It proceeds in four main steps: [1] identifying regions of similarity between query and search sequences based on consecutive word matches; [2] rescoring the initial regions and selecting best-scoring subregions; [3] optimally joining compatible initial regions to form approximate alignments; and [4] using dynamic programming to further align the highest-scoring sequences within a band centered on the best initial region. This allows FASTA to achieve faster running times than dynamic programming at the cost of some sensitivity.

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    Overview

    z Introduction
    z Heuristic approach
    z Steps in the algorithm
    Introduction

    z The FASTA algorithm is a heuristic method


    for string comparison. It was developed by
    Lipman and Pearson in 1985 and further
    improved in 1988.
    z It performs Local alignment of sequences.
    Heuristic Approach

    z Definition: A heuristic method is a method


    that uses hash coding in which the sequencce
    is broken into small “words or K-tuples”of
    specific sizes.
    z Dynamic programming methods consume
    time to analyse and search the entire
    database.Heuristic approach overcomes this
    drawback.
    FASTA - Idea -
    z Problem of Dynamic Programming
    D.P. compute the score in a lot of useless area for optimal
    sequence
    G A A T T C A G T T A
    G 1 1 1 1 1 1 1 1 1 1 1
    G 1 1 1 1 1 1 1 2 2 2 2
    A 1 2 2 2 2 2 2 2 2 2 2
    T 1 2 2 3 3 3 3 3 3 3 3
    C 1 2 2 3 3 4 4 4 4 4 4
    G 1 2 2 3 3 4 4 5 5 5 5
    A 1 2 3 3 3 4 5 5 5 5 6

    z FASTA focuses on diagonal area


    Steps in FASTA Algorithm

    z Four steps:
    1) Identify regions of similarity:
    z Using the ktup parameter which specifies #
    consecutive identities required in a match
    z 10 best diagonal regions found based on #matches
    and distance between matches
    2) Rescore regions and identify best initial regions
    z PAM250 or other scoring matrix used for rescoring the
    10 diagonal regions identified in step 1 to allow for
    conservative replacements and runs of identities
    shorter than ktup
    z For each the best diagonal regions, identify “initial
    region” that is best scoring subregion
    FASTA - Algorithm -
    z Step 1
    Find all hot-spots
    // Hot spots is pairs of words of length k that exactly match
    Sequence 1
    Hot Spots
    Sequence 2
    Steps in FASTA Algorithm

    3) Optimally join initial regions with scores > T


    ƒ Given: location of initial regions, scores, gap penalty
    ƒ Calculate an optimal alignment of initial regions as a
    combination of compatible regions with maximal score
    ƒ Use resulting score to rank the library sequences
    ƒ Selectivity degradation limited by using initial regions that
    score greater than some threshold T
    4) Align the highest scoring library sequences using
    modification of global and local alignment algorithms
    ƒ Considers all possible alignments of the query and library
    sequence that falls within a band centered around the
    highest scoring initial region
    OVERVIEW OF THE FASTA ALGORITHM

    •FastA locates regions of the query sequence and the search set
    sequence that have high densities of exact word matches.
    •For DNA sequences the word length usually used is 6.
    •The 10 highest-scoring sequence regions are saved and re-scored
    using a scoring matrix. These scores are the init1 scores
    •FastA determines if any of the initial regions from different diagonals
    may be joined together to form an approximate alignment with gaps.
    Only non-overlapping regions may be joined.
    •The score for the joined regions is the sum of the scores of the initial
    regions minus a joining penalty for each gap. The score of the highest
    scoring region, at the end of this step, is saved as the initn score.
    •FastA uses dynamic programming (Smith-Waterman algorithm ) over a
    narrow band of high scoring diagonals between the query sequence
    and the search set sequence, to produce an alignment with a new
    score.
    FASTA - Algorithm -

    z Step 1 in detail
    Use look-up Table
    Query : GAATTCAGTTA
    Sequence: G G A T C G A Dot—Matrix

    Look-up Table G A A T T C A G T T A

    Q Location G * *
    G * *
    A 2,3,7,11
    A * * * *
    C 6 T * * * *
    G 1,8 C *
    T 4,5,9,10 G * *
    A * * * *
    FASTA - Algorithm -

    zStep 2
    Score the Hot-spot and locate the ten best diagonal run.
    // There is some scoring system; ex. PAM250
    FASTA - Algorithm -

    z Step 3
    Combine sub-alignments into one alignment with GAP

    GAP

    One of local
    alignment
    FASTA - Algorithm -

    z Step 4
    Use the dynamic programming in restricted area around the best-
    score alignment to find out the higher-score alignment than the
    best-score alignment

    Width of this band


    is a parameter
    Conclusion

    Algorithm Sensitivity Running Time


    D.P 1 3
    FASTA 3 2
    BLAST 2 1
    Reference

    z N Gautham, Introduction to bioinformatics


    databases and algorithms.
    z T.K.Atwood,Parry Smith and Samiron
    Pukhan ,introduction to bioinformatics.
    Thank you

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