title: A generalized affine gap model significantly improves protein sequence alignment accuracy.
abstract: Sequence alignment underpins common tasks in molecular biology, including genome annotation, molecular phylogenetics, and homology modeling. Fundamental to sequence alignment is the placement of gaps, which represent character insertions or deletions. We assessed the ability of a generalized affine gap cost model to reliably detect remote protein homology and to produce high-quality alignments. Generalized affine gap alignment with optimal gap parameters performed as well as the traditional affine gap model in remote homology detection. Evaluation of alignment quality showed that the generalized affine model aligns fewer residue pairs than the traditional affine model but achieves significantly higher per-residue accuracy. We conclude that generalized affine gap costs should be used when alignment accuracy carries more importance than aligned sequence length.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, USA.
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Zachariah
authors.forename: Gavin E
authors.initials: GE
authors.lastname: Crooks
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Holbrook
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020690:GTPase-Activating Proteins / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D020690:GTPase-Activating Proteins; D011506:Proteins