基因组转座子鉴别与注释方法研究进展

Research Progress of Genome Transposon Identification and Annotation Methods

转座子是一类可以在基因组不同位置间移动的、重复的序列,广泛存在于真核和原核生物基因组中,并对基因组的结构、功能和进化有着重要影响。转座子鉴别与注释是基因组注释工作的重要一步,相关软件可分为3类:从头算法、基于同源性的算法和联合算法,不同的软件实现方法和功能各不相同,并各有优缺点。文中对此进行了综述,并提出在今后的开发中将会出现更多结合多种算法的综合流程程序包,它们整合多种方法的优点,针对性强,可根据不同的需求来解决实际问题。

Transposons are mobile,repetitive genetic sequences,which are prevalently present in eukaryotic and prokaryotic genomes and have a deep effect on the structure,function and evolution of genomes.Identification and annotation of transposons is an important step of genome annotation.Relevant software can be classified into three types: De novo methods,sequence homology-based methods,and coalescent methods,either of them with merits and drawbacks.Different kinds of software have different implementation methods and functions.In the future,more comprehensive software packages integrating different algorithms and endowed with the merits of these algorithms will appear and can meet different requirements.