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Bioinformatics Advance Access originally published online on June 16, 2004
Bioinformatics 2004 20(14):2288-2295; doi:10.1093/bioinformatics/bth240
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.

A practical and robust sequence search strategy for structural genomics target selection

James E. Bray 1,{dagger},*, Russell L. Marsden 1, Stuart C.G. Rison 1, Alexei Savchenko 2, Aled M. Edwards 2, Janet M. Thornton 3 and Christine A. Orengo 1

1 Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK, 2 Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, M5G 1L6, Canada and 3 EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Received on November 6, 2003; revised on February 9, 2004; accepted on February 25, 2004
Advance Access Publication August 1, 2004

Motivation: Target selection strategies for structural genomic projects must be able to prioritize gene regions on the basis of significant sequence similarity with proteins that have already been structurally determined. With the rapid development of protein comparison software a robust prioritization scheme should be independent of the choice of algorithm and be able to incorporate different sequence similarity thresholds.

Results: A robust target selection strategy has been developed that can assign a priority level to all genes in any genome. Structural assignments to genome sequences are calculated at two thresholds and six levels (1–6) describe the prioritization of all whole genes and partial gene regions. This simple two-threshold approach can be implemented with any fold recognition or homology detection algorithms. The results for 10 genomes are presented using the SSEARCH and PSI-BLAST programs.

Availability: Programs are available on request from the authors.

Contact: james.bray{at}sgc.ox.ac.uk

* To whom correspondence should be addressed.

{dagger} Present address: Structural Genomics Consortium, The Botnar Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Windmill Road, Oxford, OX4 1GA, UK.


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