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Permanent link (DOI): https://doi.org/10.7939/R31V5BF2M

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ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun Open Access

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Author or creator
Li, R.
Ye, J.
Li, S.
Wang, J.
Han, Y.
Ye, C.
Yang, H.
Yu, J.
Wong, G.K.S.
Additional contributors
Subject/Keyword
DNA
repeats
plants
rice
tools
Japonica
draft sequences
maize genome
evolution
retrotransposons
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
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.
Date created
2005
DOI
doi:10.7939/R31V5BF2M
License information
© 2005 Li et al. This is an open-access...
Rights
© 2005 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation for previous publication
Li, R., Ye, J., Li, S., Wang, J., Han, Y., Ye, C., Wang, J., et al. (2005). ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. (S. Baxter, Ed.)PLoS Computational Biology, 1(4), e43. Public Library of Science.
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