Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
Bioinformatics. 2013 Mar 1;29(5):645-6. doi: 10.1093/bioinformatics/btt009. Epub 2013 Jan 12.
gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset. It is especially useful for newly sequenced genomes that have not been well annotated. We applied gKaKs to estimate the genome-wide substitution rates in five pairs of closely related species. The average Ka and Ks computed by gKaKs were consistent with previous studies. We also compared the Ka, Ks and Ka/Ks of mouse and rat orthologous protein-coding genes estimated by gKaKs and based on the alignments generated by PAL2NAL. Results from two methods are compatible.
gKaKs is implemented in Perl and is freely available on http://longlab.uchicago.edu/?q=gKaKs. The detailed user manual is available on the website.
gKaKs 是一个基于密码子的全基因组 Ka/Ks 计算流程，它是基于四个广泛使用的程序包开发的：BLAT、BLASTALL（包括 bl2seq、formatdb 和 fastacmd）、PAML（包括 codeml 和 yn00）和 KaKs_Calculator（包括 10 种替代率估计方法）。gKaKs 可以自动检测和消除移码突变和过早终止密码子，以计算注释良好的基因组与非注释基因组甚至组装不良的支架数据集之间的替代率（Ka、Ks 和 Ka/Ks）。它特别适用于尚未得到很好注释的新测序基因组。我们应用 gKaKs 来估计五个密切相关物种的全基因组替代率。gKaKs 计算的平均 Ka 和 Ks 与先前的研究一致。我们还比较了 gKaKs 基于 PAL2NAL 生成的比对估计的小鼠和大鼠直系同源蛋白编码基因的 Ka、Ks 和 Ka/Ks。两种方法的结果是兼容的。
gKaKs 是用 Perl 编写的，可以在 http://longlab.uchicago.edu/?q=gKaKs 上免费获得。详细的用户手册可在网站上获得。
