EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference Export

@article{citeulike:20880, abstract = {EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized to achieve high prediction accuracy: (i) recognition of functionally discriminating residues (FDRs) in enzyme families obtained by a Conservation-controlled HMM Iterative procedure for Enzyme Family classification (CHIEFc), (ii) pairwise sequence comparison using a family specific Sequence Identity Threshold, (iii) recognition of FDRs in Multiple Pfam enzyme families, and (iv) recognition of multiple Prosite patterns of high specificity. For FDR (i.e. conserved positions in an enzyme family that discriminate between true and false members of the family) identification, we have developed an Evolutionary Footprinting method that uses evolutionary information from homofunctional and heterofunctional multiple sequence alignments associated with an enzyme family. The FDRs show a significant correlation with annotated active site residues. In a jackknife test, EFICAz shows high accuracy (92\%) and sensitivity (82\%) for predicting four EC digits in testing sequences that are <40\% identical to any member of the corresponding training set. Applied to Escherichia coli genome, EFICAz assigns more detailed enzymatic function than KEGG, and generates numerous novel predictions.}, author = {Tian, Weidong and Arakaki, Adrian K. and Skolnick, Jeffrey}, citeulike-article-id = {20880}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkh956}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/32/21/6226}, citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/nar/2004/00000032/00000021/art06226}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/15576349}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=15576349}, doi = {10.1093/nar/gkh956}, issn = {0305-1048}, journal = {Nucleic Acids Research}, keywords = {eficaz, enzyme, enzyme-prediction}, number = {21}, pages = {6226+}, posted-at = {2009-01-14 21:11:31}, priority = {2}, publisher = {Oxford University Press}, title = {EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference}, url = {http://dx.doi.org/10.1093/nar/gkh956}, volume = {32} }

TY - JOUR ID - citeulike:20880 L3 - citeulike-article-id:20880 N2 - EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized to achieve high prediction accuracy: (i) recognition of functionally discriminating residues (FDRs) in enzyme families obtained by a Conservation-controlled HMM Iterative procedure for Enzyme Family classification (CHIEFc), (ii) pairwise sequence comparison using a family specific Sequence Identity Threshold, (iii) recognition of FDRs in Multiple Pfam enzyme families, and (iv) recognition of multiple Prosite patterns of high specificity. For FDR (i.e. conserved positions in an enzyme family that discriminate between true and false members of the family) identification, we have developed an Evolutionary Footprinting method that uses evolutionary information from homofunctional and heterofunctional multiple sequence alignments associated with an enzyme family. The FDRs show a significant correlation with annotated active site residues. In a jackknife test, EFICAz shows high accuracy (92%) and sensitivity (82%) for predicting four EC digits in testing sequences that are <40% identical to any member of the corresponding training set. Applied to Escherichia coli genome, EFICAz assigns more detailed enzymatic function than KEGG, and generates numerous novel predictions. IS - 21 JF - Nucleic Acids Research SN - 0305-1048 TI - EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference PB - Oxford University Press VL - 32 SP - 6226 KW - eficaz KW - enzyme KW - enzyme-prediction AU - Tian, Weidong AU - Arakaki, Adrian AU - Skolnick, Jeffrey UR - http://dx.doi.org/10.1093/nar/gkh956 ER -