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/.

Figure 1

A snapshot of the SWAKK web server and sample output files. The upper part is a snapshot of the 3D analyzer web page. On the bottom are sample output files: Left, 3D provided by the 3D analyzer (when the structure is available), with amino acids colored based on inferred level of selection. Right, 2D graph ([K_A − K_S] versus window location) provided by the 1D analyzer. The example shown is the MHC glycoprotein gene (14,21) and, consistent with the previous studies, most of the sites identified under positive selection are clustered in the ARS domain.