title: Genome-wide DNA polymorphism analyses using VariScan.
abstract: BACKGROUND
  DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis.
  
  
  RESULTS
  We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.
  
  
  CONCLUSIONS
  VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain. hutter@zi.biologie.uni-muenchen.de
authors.forename: Stephan
authors.initials: S
authors.lastname: Hutter
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Vilella
authors.forename: Julio
authors.initials: J
authors.lastname: Rozas
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D016678:Genome; D006801:Humans; D051379:Mice; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D014584:User-Computer Interface