SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis | Zendy

Han Liang | Zendy; Weibin Zhou | Zendy; Laura F. Landweber | Zendy

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SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

Author(s) -

Han Liang,

Weibin Zhou,

Laura F. Landweber

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl272

Subject(s) - biology , web server , sliding window protocol , substitution (logic) , selection (genetic algorithm) , amino acid substitution , coding (social sciences) , computational biology , genetics , window (computing) , bioinformatics , the internet , gene , computer science , mutation , operating system , statistics , artificial intelligence , mathematics , programming language

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/.

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