title: WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding.
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.
  
  
  CONCLUSIONS
  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).
authors.affiliation: Korean Bioinformation Center, KRIBB, Daejeon 305-806, Korea. dolsemtl@kribb.re.kr
authors.forename: Yong Seok
authors.initials: YS
authors.lastname: Lee
authors.forename: Tae-Hyung
authors.initials: TH
authors.lastname: Kim
authors.forename: Tae-Wook
authors.initials: TW
authors.lastname: Kang
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.forename: Gwang-Sik
authors.initials: GS
authors.lastname: Shin
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D030562:Databases, Protein; D016678:Genome; D006801:Humans; D020407:Internet; D008831:Microcephaly / Q000235:genetics; D008957:Models, Genetic; D009420:Nervous System; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins; D004247:DNA