title: ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
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.
authors.affiliation: James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Jia
authors.initials: J
authors.lastname: Ye
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Yujun
authors.initials: Y
authors.lastname: Han
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D004251:DNA Transposable Elements / Q000235:genetics*; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements