ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 16184192.
- Also identified by PMC identifier 1232128.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.
Medical subject headings
- DNA Transposable Elements
- Evolution, Molecular
- Genome, Plant