ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
2005; Public Library of Science; Volume: 1; Issue: 4 Linguagem: Inglês
10.1371/journal.pcbi.0010043
ISSN1553-7358
AutoresRuiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka‐Shu Wong, Jun Wang,
Tópico(s)RNA and protein synthesis mechanisms
ResumoWe 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.
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