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

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Title
WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Author(s)
Young Seok Lee; Tae Hyung Kim; Tae Wook Kang; Won Hyong Chung; Gwang Sik Shin
Bibliographic Citation
BMC Bioinformatics, vol. 9, no. sup12, pp. s13-s13
Publication Year
2008
Abstract
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 sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins. Conclusion: WSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).
ISSN
1471-2105
Publisher
Springer-BMC
DOI
http://dx.doi.org/10.1186/1471-2105-9-S12-S13
Type
Article
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