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.
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.
Authors: Yang Zhang; Isaac A Hubner; Adrian K Arakaki; Eugene Shakhnovich; Jeffrey Skolnick Journal: Proc Natl Acad Sci U S A Date: 2006-02-14 Impact factor: 11.205
Authors: Russell L Marsden; Juan A G Ranea; Antonio Sillero; Oliver Redfern; Corin Yeats; Michael Maibaum; David Lee; Sarah Addou; Gabrielle A Reeves; Timothy J Dallman; Christine A Orengo Journal: Philos Trans R Soc Lond B Biol Sci Date: 2006-03-29 Impact factor: 6.237
Authors: Mark E Peterson; Feng Chen; Jeffery G Saven; David S Roos; Patricia C Babbitt; Andrej Sali Journal: Protein Sci Date: 2009-06 Impact factor: 6.725
Authors: Russell L Marsden; David Lee; Michael Maibaum; Corin Yeats; Christine A Orengo Journal: Nucleic Acids Res Date: 2006-02-15 Impact factor: 16.971