World Library  
Flag as Inappropriate
Email this Article

Sequence database

Article Id: WHEBN0000366847
Reproduction Date:

Title: Sequence database  
Author: World Heritage Encyclopedia
Language: English
Subject: Bioinformatics, Barcode of Life Data Systems, BLAST, Protein structure database, Peptide sequence tag
Collection: Bioinformatics, Biotechnology Databases
Publisher: World Heritage Encyclopedia

Sequence database

In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew this storage method became unsustainable.


  • Search issues 1
  • Current issues 2
  • See also 3
  • References 4
  • External links 5

Search issues

Sequence databases can be searched using a variety of methods. The most common usage is probably searching for sequences similar to a certain target protein or gene whose sequence is already known to the user. The BLAST program is a popular method of this type.

Current issues

Records in sequence databases are deposited from a wide range of sources, from individual researchers to large genome sequencing centers. As a result, the sequences themselves, and especially the biological annotations attached to these sequences, may vary in quality. There is much redundancy, as multiple labs may submit numerous sequences that are identical, or nearly identical, to others in the databases.[1]

Many annotations of the sequences are based not on laboratory experiments, but on the results of sequence similarity searches for previously-annotated sequences. Once a sequence has been annotated based on similarity to others, and itself deposited in the database, it can also become the basis for future annotations. This can lead to a transitive annotation problem because there may be several such annotation transfers by sequence similarity between a particular database record and actual wet lab experimental information.[2] Therefore, care must be taken when interpreting the annotation data from sequence databases.

See also


  1. ^
  2. ^

External links

  • European Bioinformatics Institute databases
  • NCBI completely sequenced genomes
  • Stanford Saccharomyces Genome Database
  • Protein, the NIH protein database, a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB
This article was sourced from Creative Commons Attribution-ShareAlike License; additional terms may apply. World Heritage Encyclopedia content is assembled from numerous content providers, Open Access Publishing, and in compliance with The Fair Access to Science and Technology Research Act (FASTR), Wikimedia Foundation, Inc., Public Library of Science, The Encyclopedia of Life, Open Book Publishers (OBP), PubMed, U.S. National Library of Medicine, National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health (NIH), U.S. Department of Health & Human Services, and, which sources content from all federal, state, local, tribal, and territorial government publication portals (.gov, .mil, .edu). Funding for and content contributors is made possible from the U.S. Congress, E-Government Act of 2002.
Crowd sourced content that is contributed to World Heritage Encyclopedia is peer reviewed and edited by our editorial staff to ensure quality scholarly research articles.
By using this site, you agree to the Terms of Use and Privacy Policy. World Heritage Encyclopedia™ is a registered trademark of the World Public Library Association, a non-profit organization.

Copyright © World Library Foundation. All rights reserved. eBooks from Project Gutenberg are sponsored by the World Library Foundation,
a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department.