Skip Navigation



Bioinformatics Advance Access published online on June 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti548
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/16/3429    most recent
bti548v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Smith, M.
Right arrow Articles by Ouzounis, C. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Smith, M.
Right arrow Articles by Ouzounis, C. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 8, 2005
Revised June 13, 2005
Accepted June 15, 2005

Applications note

MagicMatch - cross-referencing sequence identifiers across databases

Mike Smith 1, Victor Kunin 2, Leon Goldovsky 3, Anton J. Enright 4, and Christos A. Ouzounis 3*

1 Mullard Space Science Laboratory, Holmbury St. Mary, Dorking, Surrey RH5 6NT, UK
2 Microbial Ecology Program, DoE Joint Genome Institute, 2800 Mitchell Drive, Bldg 400-404, Walnut Creek, CA 94598, USA
3 Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
4 Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK

* To whom correspondence should be addressed.
Christos A. Ouzounis, E-mail: ouzounis{at}ebi.ac.uk


  Abstract

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. D. McDowall, M. S. Scott, and G. J. Barton
PIPs: human protein-protein interaction prediction database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D651 - D656.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. D. Karp, C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin, and N. Lopez-Bigas
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Nucleic Acids Res., October 24, 2005; 33(19): 6083 - 6089.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Goldovsky, P. Janssen, D. Ahren, B. Audit, I. Cases, N. Darzentas, A. J. Enright, N. Lopez-Bigas, J. M. Peregrin-Alvarez, M. Smith, et al.
CoGenT++: an extensive and extensible data environment for computational genomics
Bioinformatics, October 1, 2005; 21(19): 3806 - 3810.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.