线粒体基因组数据的分析方法和软件

Methods and software tools for mitochondrial genome assembly and annotation

线粒体基因组的研究已经普及,其正确的拼接和注释是所有后续研究的基础。本文以Staden Package软件为主介绍了拼接和注释的线粒体基因组的方法,同时介绍了其他常用的拼接软件ContigExpress、DNAMAN、DNASTAR、BioEdit和Sequencher,以及利用不同软件(包括DOGMA、MOSAS、MITOS、GOBASE、OGRe、MitoZoa、tRNAscan-SE、ARWEN、BLAST和MiTFi等)对线粒体基因组中的蛋白质编码基因、rRNA、tRNA和A+T富集区进行注释的方法,最后介绍了利用MEGA5软件分析线粒体基因组的组成、Sequin软件提交序列和线粒体基因组数据绘图工具(CG view、MTviz和OGDRAW)。

With the increasing popularity of mitochondrial genome studies, the correct assembly and annotation of genomes are the basis of all subsequent research into a species. Here we describe the protocols using Staden Package software to assemble and annotate the mitochondrial genome, along with other commonly used software, such as ContigExpress, DNAMAN, DNASTAR, BioEdit and Sequeneher. In addition, methods for the use of different software packages （including DOGMA.MOSAS.MITOS.GOBASE.OGRe.MitoZoa.tRNAscan-SE.ARWEN.BLAST and MiTFi） to annotate mitoehondrial genomie protein-coding genes, rRNA, tRNA and the A ＋ T region are briefly introduced. Finally, application of MEGA5 software to analyze the composition of mitochondrial genomes, Sequin software to submit sequences to GenBank, and mitochondrial genome data visualization tools （CG view. MTviz and OGDRAW） are also briefly introduced.