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.
1
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.
2
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.
3
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
4
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
10
5
Selecting a Database
Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). John Wiley & Sons Inc.
11
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
12
6
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.
13
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
14
7
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
15
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
16
8
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
17
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
18
9
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.
19
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
20
10
