LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

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/.

Figure 1.

LTR_FINDER sample output. ‘Status’ is an 11 bits binary string with each position indicating the occurrence of a certain signal. If a signal appears, the corresponding position is recorded ‘1’ and ‘0’ otherwise. From left to right, positions are as follows: [1] TG in 5′end of 5′LTR; [2] CA in 3′end of 5′LTR; [3] TG in 5′end of 3′LTR; [4] CA in 3′end of 3′LTR; [5] TSR; [6] PBS; [7] PPT; [8] RT; [9] IN(core); [10] IN(c-term) and [11] RH. ‘Score’ is an integer varying from 0 to 11. A detected signal adds 1 to its value.

Figure 2.

Diagram of two predicted elements with default parameters. Information of element 1 is shown in Figure 1. Element 2 is composed of two tandem LTR retrotransposons, which resulted from recombined insertion of a circular element. Two sets of enzyme domains are detected.

Figure 3.

Diagram of two tandem elements. Setting ‘Reliable extension’ to 0.95 and “Sharpness lower threshold’ to 0.2, the inserted element (element 3), its 5′LTR locating at 477837—478072, is reported.