MafFilter: a highly flexible and extensible multiple genome alignment files processor

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• 作者：Julien Y Dutheil (10) (11)
  Sylvain Gaillard (12) (13) (14)
  Eva H Stukenbrock (15)
  
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,260 KB
• 作者单位：Julien Y Dutheil (10) (11)
  Sylvain Gaillard (12) (13) (14)
  Eva H Stukenbrock (15)
  
  10. Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
  11. CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier 2, Place E. Bataillon, Montpellier, 34095, France
  12. INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Angers, F-49045, France
  13. Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Angers, F-49045, France
  14. UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, Université d’Angers, LUNAM Université, Angers, F-49045, France
  15. Max Planck Institute for Terrestrial Microbiology, Fungal Biodiversity Group, Marburg, Germany
  
• ISSN：1471-2164

文摘

Background Sequence alignments are the starting point for most evolutionary and comparative analyses. Full genome sequences can be compared to study patterns of within and between species variation. Genome sequence alignments are complex structures containing information such as coordinates, quality scores and synteny structure, which are stored in Multiple Alignment Format (MAF) files. Processing these alignments therefore involves parsing and manipulating typically large MAF files in an efficient way. Results MafFilter is a command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner. It provides an extensive set of tools which can be parametrized and combined by the user via option files. We demonstrate the software’s functionality and performance on several biological examples covering Primate genomics and fungal population genomics. Example analyses involve window-based alignment filtering, feature extractions and various statistics, phylogenetics and population genomics calculations. Conclusions MafFilter is a highly efficient and flexible tool to analyse multiple genome alignments. By allowing the user to combine a large set of available methods, as well as designing his/her own, it enables the design of custom data filtering and analysis pipelines for genomic studies. MafFilter is an open source software available at http://bioweb.me/maffilter.