WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding

Background: In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites. Results: This paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the subregions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Yong Seok Lee, Tae-Hyung Kim, Tae-Wook Kang, Won-Hyong Chung, Gwang-Sik Shin
• Keywords: BMCBI 2008, Natural Selection, Selection, Selection Pressures