Xu Zhao, Wang Hao
T-Life Research Center, Fudan University, 220 HanDan Road, Shanghai, 200433, China.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8. doi: 10.1093/nar/gkm286. Epub 2007 May 7.
Long terminal repeat retrotransposons (LTR elements) are ubiquitous eukaryotic transposable elements. They play important roles in the evolution of genes and genomes. Ever-growing amount of genomic sequences of many organisms present a great challenge to fast identifying them. That is the first and indispensable step to study their structure, distribution, functions and other biological impacts. However, until today, tools for efficient LTR retrotransposon discovery are very limited. Thus, we developed LTR_FINDER web server. Given DNA sequences, it predicts locations and structure of full-length LTR retrotransposons accurately by considering common structural features. LTR_FINDER is a system capable of scanning large-scale sequences rapidly and the first web server for ab initio LTR retrotransposon finding. We illustrate its usage and performance on the genome of Saccharomyces cerevisiae. The web server is freely accessible at http://tlife.fudan.edu.cn/ltr_finder/.
长末端重复逆转座子（LTR元件）是普遍存在的真核生物转座元件。它们在基因和基因组的进化中发挥着重要作用。许多生物不断增长的基因组序列数量给快速识别它们带来了巨大挑战。这是研究它们的结构、分布、功能及其他生物学影响的首要且不可或缺的步骤。然而，直到如今，用于高效发现LTR逆转座子的工具非常有限。因此，我们开发了LTR_FINDER网络服务器。给定DNA序列，它通过考虑常见结构特征准确预测全长LTR逆转座子的位置和结构。LTR_FINDER是一个能够快速扫描大规模序列的系统，也是首个用于从头发现LTR逆转座子的网络服务器。我们展示了它在酿酒酵母基因组上的使用方法和性能。该网络服务器可通过http://tlife.fudan.edu.cn/ltr_finder/免费访问。
