Accuracy of structure-based sequence alignment of automatic methods

9 years 2 months ago
Accuracy of structure-based sequence alignment of automatic methods
Background: Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy. Results: In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database (CDD) as the standard of truth. We find that 4 to 9% of the residues on average are either not aligned or aligned with more than 8 residues of shift error and that an additional 6 to 14% of residues on average are misaligned by 1–8 residues, depending on the pr...
Changhoon Kim, Byungkook Lee
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2007
Authors Changhoon Kim, Byungkook Lee
Comments (0)