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Bioinformatics Advance Access originally published online on June 16, 2005
Bioinformatics 2005 21(16):3429-3430; doi:10.1093/bioinformatics/bti548
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

MagicMatch—cross-referencing sequence identifiers across databases

Mike Smith {dagger}, Victor Kunin {ddagger}, Leon Goldovsky , Anton J. Enright § and Christos A. Ouzounis *

Computational Genomics Group, The European Bioinformatics Institute EMBL Cambridge Outstation, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed.

Motivation: At present, mapping of sequence identifiers across databases is a daunting, time-consuming and computationally expensive process, usually achieved by sequence similarity searches with strict threshold values.

Summary: We present a rapid and efficient method to map sequence identifiers across databases. The method uses the MD5 checksum algorithm for message integrity to generate sequence fingerprints and uses these fingerprints as hash strings to map sequences across databases. The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer.

Availability: MagicMatch is available at the following URL (http://cgg.ebi.ac.uk/services/magicmatch/), including an interactive service for major databases and binary downloads for widely used platforms.

Contact: ouzounis{at}ebi.ac.uk

Received on February 8, 2005; revised on June 13, 2005; accepted on June 15, 2005

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