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    Fasta and Blast

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    Sajeel75 Hanif
    FASTA and BLAST are bioinformatics tools used for sequence alignment and database searching. They use heuristic methods to quickly find regions of local similarity between sequences. BLAST finds ungapped alignments while FASTA can find similarities between less similar sequences. They allow comparison of DNA, protein, and translated nucleotide sequences against databases.

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    Fasta and Blast

    Uploaded by

    Sajeel75 Hanif
    60 views3 pages
    FASTA and BLAST are bioinformatics tools used for sequence alignment and database searching. They use heuristic methods to quickly find regions of local similarity between sequences. BLAST finds ungapped alignments while FASTA can find similarities between less similar sequences. They allow comparison of DNA, protein, and translated nucleotide sequences against databases.

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    FASTA and BLAST are bioinformatics tools used for sequence alignment and database searching. They use heuristic methods to quickly find regions of local similarity between sequences. BLAST finds ungapped alignments while FASTA can find similarities between less similar sequences. They allow comparison of DNA, protein, and translated nucleotide sequences against databases.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    60 views3 pages

    Fasta and Blast

    Uploaded by

    Sajeel75 Hanif
    FASTA and BLAST are bioinformatics tools used for sequence alignment and database searching. They use heuristic methods to quickly find regions of local similarity between sequences. BLAST finds ungapped alignments while FASTA can find similarities between less similar sequences. They allow comparison of DNA, protein, and translated nucleotide sequences against databases.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
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    BLAST and FASTA are two major algorithms used for sequence similarity searches. They use heuristic methods like word matching to quickly align sequences and identify homologous sequences. BLAST finds ungapped local alignments while FASTA can find similarities between less similar sequences.

    BLAST finds ungapped local alignments while FASTA can find similarities between less similar sequences. BLAST uses words while FASTA uses shorter k-tuples. BLAST calculates expectation values while FASTA does not.

    Variants of BLAST include BLAST-N, BLAST-P, BLAST-X, tBLAST-N and tBLAST-X which allow comparisons between different types of sequences like nucleotide to nucleotide, protein to protein or nucleotide to protein.

    FASTA and BLAST

    microbenotes.com/fasta-and-blast

    The number of DNA and protein sequences in public databases is very large.
    Searching a database involves aligning the query sequence to each sequence in the database,
    to find significant local alignment.
    BLAST and FASTA are two similarity searching programs that identify homologous DNA
    sequences and proteins based on the excess sequence similarity.
    They provide facilities for comparing DNA and proteins sequences with the existing DNA
    and protein databases.
    They are two major heuristic algorithms for performing database searches.

    Working of FASTA and BLAST


    FASTA and BLAST are the software tools used in bioinformatics. Both BLAST and FASTA
    use a heuristic word method for fast pairwise sequence alignment.
    It works by finding short stretches of identical or nearly identical letters in two sequences.
    These short strings of characters are called words.
    The basic assumption is that two related sequences must have at least one word in common.
    By first identifying word matches, a longer alignment can be obtained by extending
    similarity regions from the words.
    Once regions of high sequence similarity are found, adjacent high-scoring regions can be
    joined into a full alignment.

    The main difference between BLAST and FASTA is that BLAST is mostly involved in finding of
    ungapped, locally optimal sequence alignments whereas FASTA is involved in finding similarities
    between less similar sequences.

    BLAST (Basic Local Alignment Search Tool)

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    The BLAST program was developed by Stephen Altschul of NCBI in 1990 and has since
    become one of the most popular programs for sequence analysis.
    BLAST uses heuristics to align a query sequence with all sequences in a database.
    The objective is to find high-scoring ungapped segments among related sequences. The
    existence of such segments above a given threshold indicates pairwise similarity beyond
    random chance, which helps to discriminate related sequences from unrelated sequences in
    a database.
    BLAST is popular as a bioinformatics tool due to its ability to identify regions of local
    similarity between two sequences quickly. BLAST calculates an expectation value, which
    estimates the number of matches between two sequences. It uses the local alignment of
    sequences.

    Variants of BLAST
    BLAST-N: compares nucleotide sequence with nucleotide sequences
    BLAST-P: compares protein sequences with protein sequences
    BLAST-X: Compares nucleotide sequences against the protein sequences
    tBLAST-N: compares the protein sequences against the six frame translations of nucleotide
    sequences
    tBLAST-X: Compares the six frame translations of nucleotide sequence against the six
    frame translations of protein sequences.

    FASTA
    FASTA stands for fast-all” or “FastA”.
    It was the first database similarity search tool developed, preceding the development of
    BLAST.
    FASTA is another sequence alignment tool which is used to search similarities between
    sequences of DNA and proteins.
    FASTA uses a “hashing” strategy to find matches for a short stretch of identical residues
    with a length of k. The string of residues is known as ktuples or ktups, which are equivalent
    to words in BLAST, but are normally shorter than the words.
    Typically, a ktup is composed of two residues for protein sequences and six residues for
    DNA sequences.
    The query sequence is thus broken down into sequence patterns or words known as k-tuples
    and the target sequences are searched for these k-tuples in order to find the similarities
    between the two.
    FASTA is a fine tool for similarity searches.

    These methods are not guaranteed to find the optimal alignment or true homologs, but are 50–
    100 times faster than dynamic programming.

    References
    1. Xiong J. (2006). Essential Bioinformatics. Texas A & M University. Cambridge University
    Press.
    2. Arthur M Lesk (2014). Introduction to bioinformatics. Oxford University Press. Oxford,
    United Kingdom
    3. http://pediaa.com/difference-between-blast-and-fasta/#BLAST
    4. https://embnet.vital-it.ch/CoursEMBnet/Basel03/slides/BLAST_FASTA.pdf

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    5. https://www.slideshare.net/avrilcoghlan/blast-16572940
    6. https://www.cs.helsinki.fi/bioinformatiikka/mbi/courses/0708/itb/slides/itb0708_slides_83-
    116.pdf
    7. https://blast.ncbi.nlm.nih.gov/Blast.cgi?
    CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp

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