Identification of retrotransposons in large genomes

Question

[Leszek]

I would like to characterise retroelements (retrotransposons) across several plant genomes. I don't have any experience with identification and classification of repetitive elements. Can you recommend me some tools or some good reads focusing on the topic?

EDIT:

LTRharvest is a tool specifically designed to find LTR retrotransposons in large genomes.

Also RepeatMasker detect retrotransposons among many other repetitive sequences.

Answer 1

[AndreiR]

Hello,

My first shot would be RepeatMasker. Genomes in GoldenPath are scanned for repetitive elements with it.

Although from 2004, this paper has interesting methods.

Transposable element annotation of the rice genome.

From abstract:

We used a combination of computational approaches to annotate the TEs in the finished genome of Oryza sativa ssp. japonica. In this paper, we discuss the strengths and the weaknesses of the annotation methods used. These approaches included: the default configuration of RepeatMasker using cross_match, an implementation of the Smith-Waterman-Gotoh algorithm; RepeatMasker using WU-BLAST for similarity searching; and the HMMER package, used to search for TEs with profile HMMs.

[Leszek]

Thanks Andrei, I've tried RepeatMasker and it worked quite well. I've also used LTRharvest (http://www.zbh.uni-hamburg.de/?id=206), which is specifically designed to find LTR retrotransposons.