title: SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.
abstract: We present a bioinformatic web server (SWAKK) for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure. In addition, for comparison or when a reference structure is unavailable, the server can also perform a sliding window analysis on the primary sequence. The SWAKK web server is available at http://oxytricha.princeton.edu/SWAKK/.
authors.affiliation: Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Liang
authors.forename: Weihua
authors.initials: W
authors.lastname: Zhou
authors.forename: Laura F
authors.initials: LF
authors.lastname: Landweber
mesh_terms: D019943:Amino Acid Substitution; D019295:Computational Biology / Q000379:methods; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012641:Selection, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins