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

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 i...

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Detalles Bibliográficos
Autores principales: Li, Ruiqiang, Ye, Jia, Li, Songgang, Wang, Jing, Han, Yujun, Ye, Chen, Wang, Jian, Yang, Huanming, Yu, Jun, Wong, Gane Ka-Shu, Wang, Jun
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2005
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1232128/
https://www.ncbi.nlm.nih.gov/pubmed/16184192
http://dx.doi.org/10.1371/journal.pcbi.0010043
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author Li, Ruiqiang
Ye, Jia
Li, Songgang
Wang, Jing
Han, Yujun
Ye, Chen
Wang, Jian
Yang, Huanming
Yu, Jun
Wong, Gane Ka-Shu
Wang, Jun
author_facet Li, Ruiqiang
Ye, Jia
Li, Songgang
Wang, Jing
Han, Yujun
Ye, Chen
Wang, Jian
Yang, Huanming
Yu, Jun
Wong, Gane Ka-Shu
Wang, Jun
author_sort Li, Ruiqiang
collection PubMed
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.
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spelling pubmed-12321282005-10-03 ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun Li, Ruiqiang Ye, Jia Li, Songgang Wang, Jing Han, Yujun Ye, Chen Wang, Jian Yang, Huanming Yu, Jun Wong, Gane Ka-Shu Wang, Jun PLoS Comput Biol Research Article 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. Public Library of Science 2005-09 2005-09-23 /pmc/articles/PMC1232128/ /pubmed/16184192 http://dx.doi.org/10.1371/journal.pcbi.0010043 Text en Copyright: © 2005 Li et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Li, Ruiqiang
Ye, Jia
Li, Songgang
Wang, Jing
Han, Yujun
Ye, Chen
Wang, Jian
Yang, Huanming
Yu, Jun
Wong, Gane Ka-Shu
Wang, Jun
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title_full ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title_fullStr ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title_full_unstemmed ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title_short ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
title_sort reas: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1232128/
https://www.ncbi.nlm.nih.gov/pubmed/16184192
http://dx.doi.org/10.1371/journal.pcbi.0010043
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