Department of Computer Science, Northern Illinois University, DeKalb, IL 60115, USA.
Bioinformatics. 2011 Dec 1;27(23):3266-75. doi: 10.1093/bioinformatics/btr566. Epub 2011 Oct 12.
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.
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.
Software tools, scripts and result data are available at http://faculty.cs.niu.edu/~hou/PicoInversion.html.
已经有几项关于人类和黑猩猩之间微倒位的研究，但它们的结果存在很大差异。此外，它们都依赖于比对程序或现有的比对结果来识别倒位。然而，核心比对程序并没有考虑非常小的倒位。因此，它们的分析无法发现太小而无法被经典比对器检测到的倒位。我们将这种倒位称为皮克倒位。
我们重新分析了 UCSC 基因组浏览器中人类-黑猩猩的比对，以寻找微在位倒位，并使用似然比检验筛选皮克在位倒位。我们报告说，人类和黑猩猩之间的在位倒位数量远远超过之前的发现。我们还介绍了用于检测近缘物种之间皮克在位倒位的软件工具 PicoInversionMiner。
软件工具、脚本和结果数据可在 http://faculty.cs.niu.edu/~hou/PicoInversion.html 获得。
