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Bioinformatics Advance Access published online on January 3, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl637
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 12, 2006
Revised December 11, 2006
Accepted December 12, 2006

Applications note

MinSet : A general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database

Alessandro Pandini 1, Laura Bonati 1, Franca Fraternali 2, and Jens Kleinjung 3 *

1 Dipartimento di Scienze dell'Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Milano, Italy
2 Bioinformatics Unit, King's College, London, UK
3 Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.

* To whom correspondence should be addressed.
Jens Kleinjung, E-mail: jkleinj{at}nimr.mrc.ac.uk


  Abstract

Motivation: The size of current protein databases is a challenge for many Bioinformatics applications, both in terms of processing speed and information redundancy. It may be therefore desirable to efficiently reduce the database of interest to a maximally representative subset.

Results: The MinSet method employs a combination of a Suffix Tree and a Genetic Algorithm for the generation, selection and assessment of database subsets. The approach is generally applicable to any type of string-encoded data, allowing for a drastic reduction of the database size whilst retaining most of the information contained in the original set. We demonstrate the performance of the method on a database of protein domain structures encoded as strings. We used the SCOP40 domain database by translating protein structures into character strings by means of a structural alphabet and by extracting optimised subsets according to an entropy score that is based on a constant-length fragment dictionary. Therefore, optimised subsets are maximally representative for the distribution and range of local structures. Subsets containing only 10% of the SCOP structure classes show a coverage of > 90% for fragments of length 1-4.

Availability: http://mathbio.nimr.mrc.ac.uk/~jkleinj/MinSet.

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Charlie Hodgman
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