Work

Pico-inplace-inversions between human and chimpanzee

Year: 2011

Type: article

Abstract: MOTIVATION: There have been several studies on the micro-inversions between human and chimpanzee, but there are large discrepancies among their results. Furthermore, all of them rely on alignment procedures or existing alignment results to identify inversions. However, the core alignment procedures do not take very small inversions into consideration. Therefore, their analyses cannot find inversions that are too small to be detected by a classic aligner. We call such inversions pico-inversions. RESULTS: We re-analyzed human-chimpanzee alignment from the UCSC Genome Browser for micro-inplace-inversions and screened for pico-inplace-inversions using a likelihood ratio test. We report that the quantity of inplace-inversions between human and chimpanzee is substantially greater than what had previously been discovered. We also present the software tool PicoInversionMiner to detect pico-inplace-inversions between closely related species. AVAILABILITY: Software tools, scripts and result data are available at http://faculty.cs.niu.edu/~hou/PicoInversion.html. CONTACT: [email protected].

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btr566

Authors: Minmei Hou, Ping Yao, Angela Antonou, Mitrick A. Johns

Institution: Northern Illinois University

Language: English

Topic: Genome Rearrangement Algorithms

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Northern Illinois University, National Human Genome Research Institute

Award: Detect small and very small in-space inversions and improve alignment quality