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Related Experiment Videos

Database searching with DNA and protein sequences: an introduction.

C Sansom1

  • 1Department of Crystallography, Birkbeck College, London, WC1E 7HX UK. c.sansom@mail.cryst.bbk.ac.uk

Briefings in Bioinformatics
|July 27, 2001
PubMed
Summary

This review provides practical guidelines for experimental biologists on sequence database searching. It covers essential tools like BLAST and FASTA, and key databases such as EMBL, GenBank, DDBJ, Swiss-Prot, and TrEMBL.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Sequence database searching is crucial for experimental biologists to analyze genetic and protein data.
  • Understanding current practices and available resources is essential for efficient biological research.

Purpose of the Study:

  • To provide practical guidelines for experimental biologists on sequence database searching.
  • To review current practices, principles, and available databases for sequence analysis.

Main Methods:

  • Detailed description of commonly used algorithms: Basic Local Alignment Search Tool (BLAST) and FASTA.
  • Enumeration of public domain sequence databases, including DNA (EMBL, GenBank, DDBJ) and protein (Swiss-Prot, TrEMBL).
  • Comparison of scoring matrices for protein sequence comparison, focusing on PAM and BLOSUM series.

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Main Results:

  • Identified key public domain databases (EMBL, GenBank, DDBJ, Swiss-Prot, TrEMBL) as primary resources.
  • Detailed explanation of BLAST and FASTA algorithms, highlighting their utility in sequence similarity searches.
  • Comparison of scoring matrices (PAM, BLOSUM) for evaluating amino acid substitutions in protein searches.

Conclusions:

  • Experimental biologists can benefit from understanding sequence database searching principles and tools.
  • Effective utilization of databases like EMBL, GenBank, DDBJ, Swiss-Prot, and TrEMBL, along with algorithms like BLAST and FASTA, enhances biological research.
  • Knowledge of scoring matrices aids in accurate protein sequence comparison and analysis.