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Finding Structural Variations with Pair-End Sequences and a Sliding Window

Posted in research by ryanlayer on October 19, 2009

This is a short description of the algorithm used in the paper Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.

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Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.

Posted in research by ryanlayer on October 8, 2009

Nucleic Acids Res. 2009 Aug 26.

Paper

Abstract

Paired end mapping of chromosomal fragments has been used in human cells to identify numerous structural variations in chromosomes of individuals and of cancer cell lines; however, the molecular, biological and bioinformatics methods for this technology are still in development. Here, we present a parallel bioinformatics approach to analyze chromosomal paired-end tag (ChromPET) sequence data and demonstrate its application in identifying gene rearrangements in the model organism Saccharomyces cerevisiae. We detected several expected events, including a chromosomal rearrangement of the nonessential arm of chromosome V induced by selective pressure, rearrangements introduced during strain construction and gene conversion at the MAT locus. In addition, we discovered several unannotated Ty element insertions that are present in the reference yeast strain, but not in the reference genome sequence, suggesting a few revisions are necessary in the latter. These data demonstrate that application of the chromPET technique to a genetically tractable organism like yeast provides an easy screen for studying the mechanisms of chromosomal rearrangements during the propagation of a species.