Question: Identification of retrotransposons in large genomes
1
gravatar for Leszek
2.8 years ago by
Leszek3.9k
IIMCB, Poland
Leszek3.9k wrote:

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. 

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Leszek3.9k
1
gravatar for AndreiR
2.8 years ago by
AndreiR50
.
AndreiR50 wrote:

Hello,

My first shot would be RepeatMasker (http://www.repeatmasker.org/). Genomes in GoldenPath are scanned for repetitive elements with it.

Although from 2004, this paper have a interesting methods : http://www.ncbi.nlm.nih.gov/pubmed/14734305

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."

ADD COMMENTlink written 2.8 years ago by AndreiR50
1

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. 

ADD REPLYlink written 2.8 years ago by Leszek3.9k
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