[Computational approaches for identification and classification of transposable elements in eukaryotic genomes].
Repetitive sequences (repeats) represent a significant fraction of the eukaryotic genomes and can be divided into tandem repeats, segmental duplications, and interspersed repeats on the basis of their sequence characteristics and how they are formed. Most interspersed repeats are derived from transposable elements (TEs). Eukaryotic TEs have been subdivided into two major classes according to the intermediate they use to move. The transposition and amplification of TEs have a great impact on the evolution of genes and the stability of genomes. However, identification and classification of TEs are complex and difficult due to the fact that their structure and classification are complex and diverse compared with those of other types of repeats. Here, we briefly introduced the function and classification of TEs, and summarized three different steps for identification, classification and annotation of TEs in eukaryotic genomes: (1) assembly of a repeat library, (2) repeat correction and classification, and (3) genome annotation. The existing computational approaches for each step were summarized and the advantages and disadvantages of the approaches were also highlighted in this review. To accurately identify, classify, and annotate the TEs in eukaryotic genomes requires combined methods. This review provides useful information for biologists who are not familiar with these approaches to find their way through the forest of programs.
The Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China. hongen_xu@hotmail.com
Hong-En
HE
Xu
Hua-Hao
HH
Zhang
Min-Jin
MJ
Han
Yi-Hong
YH
Shen
Xian-Zhi
XZ
Huang
Zhong-Huai
ZH
Xiang
Ze
Z
Zhang
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements; D056890:Eukaryota / Q000235:genetics*; D015723:Gene Library; D016678:Genome; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software
D004251:DNA Transposable Elements