Bioinformatics Vol. 16 no. 10 2000
Pages 915-922
© 2000 Oxford University Press
Original Paper |
CAST: an iterative algorithm for the complexity analysis of sequence tracts
1 Department of Cell Biology and Biophysics,
Faculty of Biology, University of Athens, Athens GR-15701, Greece
2 Computational Genomics Group
3 SRS Team, Research Programme, The European
Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10
1SD, UK
4 Millennium Pharmaceuticals Inc., 640
Memorial Drive, Cambridge, MA 02139, USA
Received on February 8, 2000
; revised on April 11, 2000
; accepted on April 18, 2000
Motivation: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions.
Results: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith–Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions.
Availability: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/
Contact: ouzounis{at}ebi.ac.uk
To whom correspondence should be addressed.
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