Abstract
BackgroundIn 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.ResultsThis 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.ConclusionWSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).
Highlights
In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting
WSPMaker (Window-sliding Selection pressure Plot Maker) uses the ClustalW sequence alignment tool [8]. It requires two orthologous mRNA sequences. It translates them into protein sequences and chooses the longest open reading frame (ORF) by a user-selected genetic code table
This step is skipped if users submit their own alignment of orthologous coding DNA sequences (CDSs)
Summary
WSPMaker (Window-sliding Selection pressure Plot Maker) uses the ClustalW sequence alignment tool [8]. WSPMaker provides a choice of one of the 17 NCBI genetic codes [10] for automatically generated codon-based alignment after translating orthologous CDSs. There are two additional advanced options: 'Single Size' and 'User Defined Size.' If users select 'Single Size,' they can choose one of three models to detect the sites that are under significant selection pressure. The second section contains a Ka/Ks graph, which shows the window-sliding selection pressure between two orthologous coding genes that have been entered in the input page. To detect interesting evolutionary signatures, a good statistical power and other test methods are necessary One such method is our MSPMaker, which scans and calculates selection pressure (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs). The domain information provided by WSPMaker lets users compare the selection pressure on the protein domain regions and understand which particular positions are functionally important
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