A comprehensive system for evaluation of remote sequence similarity detection

Background: Accurate and sensitive performance evaluation is crucial for both effective development of better structure prediction methods based on sequence similarity, and for the comparative analysis of existing methods. Up to date, there has been no satisfactory comprehensive evaluation method that (i) is based on a large and statistically unbiased set of proteins with clearly defined relationships; and (ii) covers all performance aspects of sequence-based structure predictors, such as sensitivity and specificity, alignment accuracy and coverage, and structure template quality. Results: With the aim of designing such a method, we (i) select a statistically balanced set of divergent protein domains from SCOP, and define similarity relationships for the majority of these domains by complementing the best of information available in SCOP with a rigorous SVM-based algorithm; and (ii) develop protocols for the assessment of similarity detection and alignment quality from several complem...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Yuan Qi, Ruslan Sadreyev, Yong Wang, Bong-Hyun Kim, Nick V. Grishin
• Keywords: BMCBI 2007, Evaluation, Satisfactory Comprehensive Evaluation, Similarity Detection