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Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q
Author(s) -
Kihara Daisuke,
Skolnick Jeffrey
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20044
Subject(s) - orfs , threading (protein sequence) , genome , structural genomics , computational biology , biology , function (biology) , genetics , structure function , protein structure , algorithm , computer science , open reading frame , physics , gene , peptide sequence , biochemistry , particle physics
The genome scale threading of five complete microbial genomes is revisited using our state‐of‐the‐art threading algorithm, PROSPECTOR_Q. Considering that structure assignment to an ORF could be useful for predicting biochemical function as well as for analyzing pathways, it is important to assess the current status of genome scale threading. The fraction of ORFs to which we could assign protein structures with a reasonably good confidence level to each genome sequences is over 72%, which is significantly higher than earlier studies. Using the assigned structures, we have predicted the function of several ORFs through “single‐function” template structures, obtained from an analysis of the relationship between protein fold and function. The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.