Premium
STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile–profile scoring
Author(s) -
Debe Derek A.,
Danzer Joseph F.,
Goddard William A.,
Poleksic Aleksandar
Publication year - 2006
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.21049
Subject(s) - multiple sequence alignment , computer science , dynamic programming , benchmark (surveying) , alignment free sequence analysis , structural alignment , smith–waterman algorithm , sequence alignment , homology (biology) , pattern recognition (psychology) , artificial intelligence , data mining , algorithm , peptide sequence , biology , biochemistry , geodesy , gene , geography
STRUCTFAST is a novel profile—profile alignment algorithm capable of detecting weak similarities between protein sequences. The increased sensitivity and accuracy of the STRUCTFAST method are achieved through several unique features. First, the algorithm utilizes a novel dynamic programming engine capable of incorporating important information from a structural family directly into the alignment process. Second, the algorithm employs a rigorous analytical formula for profile–profile scoring to overcome the limitations of ad hoc scoring functions that require adjustable parameter training. Third, the algorithm employs Convergent Island Statistics (CIS) to compute the statistical significance of alignment scores independently for each pair of sequences. STRUCTFAST routinely produces alignments that meet or exceed the quality obtained by an expert human homology modeler, as evidenced by its performance in the latest CAFASP4 and CASP6 blind prediction benchmark experiments. Proteins 2006. © 2006 Wiley‐Liss, Inc.