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. 2008 Dec 12;9 Suppl 12(Suppl 12):S13.
doi: 10.1186/1471-2105-9-S12-S13.

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

Yong Seok Lee  1 , Tae-Hyung Kim, Tae-Wook Kang, Won-Hyong Chung, Gwang-Sik Shin
Affiliations

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

Yong Seok Lee et al. BMC Bioinformatics. .

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).

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Figures

Figure 1
Figure 1
A schematic overview of the WSPMaker.
Figure 2
Figure 2
An example of the WSPMaker main output page. The calculated Ka/Ks ratios are plotted as slim bars within a default sliding window size. A) WSPMaker results for MCPH1. B) WSPMaker results for CHRM5.
Figure 3
Figure 3
An example of the WSPMaker main input page. Users can paste in or upload sequences to calculate the Ka/Ks values of sub-regions in a CDS.
See this image and copyright information in PMC

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