FASTA Servers for Sequence Similarity Search

  • Biju Issac
  • Gajendra P. S. Raghava
Part of the Springer Protocols Handbooks book series (SPH)


In the last few years, many eukaryotic (including human and mouse) and prokaryotic genomes have been either completely sequenced or are under sequencing (1, 2, 3). In the coming 5–10 yr, most of the known organisms will have been sequenced. This has and will lead to exponential growth in nucleotide and protein databases over the years; for example, International Nucleotide Sequence Databases (INSD), composed of DDBJ (, EMBL Bank (, and GenBank (, had released more than 30 million entries by the end of 2003 (4). The availability of these increasingly expanding databases poses a major challenge to bioinformatics experts for developing effective programs or Web servers that extract maximum information from these databases. Database similarity search is perhaps the fastest, cheapest, and most powerful such experiment a biologist can conduct. As the databases become more complete, a sequence similarity search is more likely to reveal database sequences with statistically significant similarity, and thus inferred homology, to a query sequence. Though sharing significant sequence similarity is no guarantee of shared function, the availability of similar sequences is proving useful in discovering relationships between newly sequenced proteins or genes and various classes in the databases (5, 6, 7).


Multiple Sequence Alignment Query Sequence Basic Local Alignment Search Tool Library Sequence Initial Region 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Biju Issac
    • 1
  • Gajendra P. S. Raghava
    • 1
  1. 1.Institute of Microbial TechnologyChandigarhIndia

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