Aligning Two Genomic Sequences That Contain Duplications

  • Authors:

  • Minmei Hou;Cathy Riemer;Piotr Berman;Ross C. Hardison;Webb Miller

  • Affiliations:

  • Dept. of Computer Science, Northern Illinois University, USA;Center for Comparative Genomics and Bioinformatics, Penn State University, USA;Dept. of Computer Science and Engineering, Penn State University, USA;Center for Comparative Genomics and Bioinformatics, Penn State University, USA and Dept. of Biochemistry and Molecular Biology, Penn State University, USA;Center for Comparative Genomics and Bioinformatics, Penn State University, USA and Dept. of Computer Science and Engineering, Penn State University, USA and Dept. of Biology, Penn State University ...

  • Venue:
  • RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
  • Year:
  • 2009

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Abstract

It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.