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Bioinformatics Vol. 16 no. 5 2000
Pages 458-464
© 2000 Oxford University Press

RSDB: representative protein sequence databases have high information content

Jong Park 1, Liisa Holm 1, Andreas Heger 1 and Cyrus Chothia 2

1 The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK
2 LMB, MRC Centre, Hills Road, Cambridge, CB2 2QH, UK

Received on October 28, 1999 ; revised on December 9, 1999 ; accepted on December 7, 1999

Motivation: Biological sequence databases are highly redundant for two main reasons: 1. various databanks keep redundant sequences with many identical and nearly identical sequences 2. natural sequences often have high sequence identities due to gene duplication. We wanted to know how many sequences can be removed before the databases start losing homology information. Can a database of sequences with mutual sequence identity of 50% or less provide us with the same amount of biological information as the original full database?

Results: Comparisons of nine representative sequence databases (RSDB) derived from full protein databanks showed that the information content of sequence databases is not linearly proportional to its size. An RSDB reduced to mutual sequence identity of around 50% (RSDB50) was equivalent to the original full database in terms of the effectiveness of homology searching. It was a third of the full database size which resulted in a six times faster iterative profile searching. The RSDBs are produced at different granularity for efficient homology searching.

Availability: All the RSDB files generated and the full analysis results are available through internet: ftp://ftp.ebi.ac.uk/pub/contrib/jong/RSDB/http://cyrah.ebi.ac.uk:1111/Proj/Bio/RSDB

Contact: jong{at}biosophy.org


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