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: mhou@cs.niu.edu.
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: mhou@cs.niu.edu.
Authors: W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler Journal: Genome Res Date: 2002-06 Impact factor: 9.043
Authors: W James Kent; Robert Baertsch; Angie Hinrichs; Webb Miller; David Haussler Journal: Proc Natl Acad Sci U S A Date: 2003-09-19 Impact factor: 11.205
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Authors: Hreinn Stefansson; Agnar Helgason; Gudmar Thorleifsson; Valgerdur Steinthorsdottir; Gisli Masson; John Barnard; Adam Baker; Aslaug Jonasdottir; Andres Ingason; Vala G Gudnadottir; Natasa Desnica; Andrew Hicks; Arnaldur Gylfason; Daniel F Gudbjartsson; Gudrun M Jonsdottir; Jesus Sainz; Kari Agnarsson; Birgitta Birgisdottir; Shyamali Ghosh; Adalheidur Olafsdottir; Jean-Baptiste Cazier; Kristleifur Kristjansson; Michael L Frigge; Thorgeir E Thorgeirsson; Jeffrey R Gulcher; Augustine Kong; Kari Stefansson Journal: Nat Genet Date: 2005-01-16 Impact factor: 38.330