Bio16 Computational Biology

Basic Local Alignment Search Tool (BLAST)

Prepared by:
Joseph Martin Q. Paet
Biology Department, College of Science
Bicol University

BLAST

Basic Local Alignment Search Tool

main NCBI tool for comparing a protein or DNA sequence (query) to
other database sequences (target) = reveals related sequences

finds regions of local similarity between sequences having both

speed and sensitivity (heuristic local alignment)

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
Sansom, C. (2000). Database searching with DNA and protein sequences: An introduction. Briefings in bioinformatics, 1(1), 22-32.

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 BLAST Algorithm

Sansom, C. (2000). Database searching with DNA and protein sequences: An introduction. Briefings in bioinformatics, 1(1), 22-32.

BLAST Algorithm

Sansom, C. (2000). Database searching with DNA and protein sequences: An introduction. Briefings in bioinformatics, 1(1), 22-32.

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 BLAST Algorithm

Sansom, C. (2000). Database searching with DNA and protein sequences: An introduction. Briefings in bioinformatics, 1(1), 22-32.

BLAST: Uses

Determining what orthologs and paralogs are known for a

particular protein or nucleic acid sequence.
Determining what proteins or genes are present in a particular
organism.
Determining the identity of a DNA or protein sequence.
Discovering new genes.
Determining what variants have been described for a particular
gene or protein.
Investigating expressed sequence tags (ESTs) that may exhibit
alternative splicing.
Exploring amino acid residues that are important in a protein’s
function and/or structure.

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

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 BLAST: 4 Key Steps

Specifying Sequence of Interest

Selecting BLAST Program

Selecting a Database

a: Selecting Optional Search Parameters

b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

Specifying Sequence of Interest

Data Inputs:
cutting and pasting DNA or protein sequence
using an accession number

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 Selecting BLAST Program

Family of 5 Programs

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

Selecting a Database

National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 Selecting a Database

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

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a: Selecting Optional Search Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 a: Selecting Optional Search Parameters

McGinnis, S., & Madden, T. L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic acids research, 32(suppl_2), W20-W25.

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b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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b: Selecting Formatting Parameters

Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information. https://blast.ncbi.nlm.nih.gov/Blast.cgi

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 BLAST: Search Statistics

E = expect value; the number of different alignments with scores

equivalent to or better than S (similarity score) that are expected to
occur by chance in a database search; affected by the scoring
system, size of the database, and size of the query
E is related to p-value = probability of a chance alignment
occurring with the score in question or better; closer to zero the
better
Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

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Bio16 Computational Biology

Basic Local Alignment Search Tool (BLAST)

References:
Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.

Sansom, C. (2000). Database searching with DNA and protein sequences: An introduction. Briefings in bioinformatics, 1(1), 22-32.

McGinnis, S., & Madden, T. L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic acids research, 32(suppl_2), W20-W25.

National Center for Biotechnology Information. (2023). BLAST: Basic Local Alignment Search Tool. National Center for Biotechnology Information.
https://blast.ncbi.nlm.nih.gov/Blast.cgi

Prepared by:
Joseph Martin Q. Paet
Biology Department, College of Science
Bicol University

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