LTR_FINDER: An Efficient Tool for the Prediction of Full-Length LTR Retrotransposons

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8. doi: 10.1093/nar/gkm286. Epub 2007 May 7.

Abstract

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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods*
  • Database Management Systems*
  • Databases, Nucleic Acid
  • Information Storage and Retrieval / methods*
  • Internet
  • Molecular Sequence Data
  • Retroelements / genetics*
  • Saccharomyces cerevisiae / genetics
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods
  • Software
  • Terminal Repeat Sequences / genetics*

Substances

  • Retroelements