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


BACKGROUND
Programs are available on request from the authors.
Bray
James E
JE
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. james.bray@sgc.ox.ac.uk
Marsden
Russell L
RL
Rison
Stuart C G
SC
Savchenko
Alexei
A
Edwards
Aled M
AM
Thornton
Janet M
JM
Orengo
Christine A
CA
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D018390:Gene Targeting / Q000379:methods*; D005796:Genes / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship