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Bioinformatics Vol. 16 no. 2 2000
Pages 104-110
© 2000 Oxford University Press

Sequence search algorithm assessment and testing toolkit (SAT)

Jong Park 1, Liisa Holm 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

Motivation: The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm.

Results: An analysis on two different data sets was carried out using the SAT package. It compared the performance of a full protein sequence database (RSDB100) with a non-redundant representative sequence database derived from it (RSDB50). The performance measurement indicated that the full database is sub-optimal for a homology search. This result justifies the use of much smaller and faster RSDB50 than RSDB100 for the SAT.

Availability: A web site is up. The whole package is accessible via www and ftp. ftp://ftp.ebi.ac.uk/pub/contrib/jong/SAThttp://cyrah.ebi.ac.uk:1111/Proj/Bio/SAThttp://www.mrc-lmb.cam.ac.uk/genomes/SATIn the package, some previous assessment results produced by the package can also be found for reference.

Contact: jong{at}ebi.ac.uk

Received on June 24, 1999 ; revised on August 18, 1999 ; accepted on September 10, 1999

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