作者
Chengjun Zhang, Jun Wang, Manyuan Long, Chuanzhu Fan
发表日期
2013/1/12
期刊
Bioinformatics
卷号
29
期号
5
页码范围
645-646
出版商
Oxford University Press
简介
Summary: 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 …
学术搜索中的文章
C Zhang, J Wang, M Long, C Fan - Bioinformatics, 2013