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WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Yong Seok Lee1, Tae-Hyung Kim, Tae-Wook Kang
1Korean Bioinformation Center, KRIBB, Daejeon 305-806, Korea. dolsemtl@kribb.re.kr
BMC Bioinformatics
|December 19, 2008
Summary
This study introduces WSPMaker, a web tool for analyzing adaptive protein evolution. It calculates selection pressures (Ka/Ks) in specific DNA regions, aiding the detection of natural selection acting on protein-coding sites.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Bioinformatics
Background:
- Detecting natural selection on protein-coding sites is crucial for understanding adaptive evolution.
- The ratio of non-synonymous to synonymous substitutions (Ka/Ks) generally estimates selection for gene regions.
- Individual amino acids have varied functions, necessitating site-specific selection analysis, especially for domain sites.
Purpose of the Study:
- To develop a web-based tool for calculating selection pressures in sub-regions of protein-coding DNA sequences.
- To enable detailed investigation of adaptive protein evolution and selective constraints at a finer scale.
Main Methods:
- Development of WSPMaker, a web tool utilizing a sliding window approach on DNA sequences.
- Calculation of selection pressures (Ka/Ks) within user-defined window lengths.
- Integration of Pfam HMM models to identify conserved residues within orthologous proteins.
Main Results:
- WSPMaker provides a method for scanning and calculating Ka/Ks ratios in specific sub-regions of two coding DNA sequences.
- The tool facilitates the analysis of selective constraints across different regions of orthologous genes.
- It supports various evolutionary models and user-defined parameters like window size.
Conclusions:
- WSPMaker is a valuable web-based resource for analyzing selection pressures in protein-coding DNA sequences.
- The tool aids in identifying sites under varying selective constraints, contributing to the study of adaptive evolution.
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