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

@article{citeulike:2245018, 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.}, author = {Li, Ruiqiang and Ye, Jia and Li, Songgang and Wang, Jing and Han, Yujun and Ye, Chen and Wang, Jian and Yang, Huanming and Yu, Jun and Wong, Gane K. and Wang, Jun}, citeulike-article-id = {2245018}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0010043}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16184192}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16184192}, day = {23}, doi = {10.1371/journal.pcbi.0010043}, issn = {1553-7358}, journal = {PLoS Comput Biol}, keywords = {de-novo, repeat}, month = {September}, number = {4}, pages = {e43+}, posted-at = {2009-11-02 16:41:00}, priority = {2}, publisher = {Public Library of Science}, title = {ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun}, url = {http://dx.doi.org/10.1371/journal.pcbi.0010043}, volume = {1}, year = {2005} }

TY - JOUR ID - citeulike:2245018 L3 - citeulike-article-id:2245018 N2 - 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. IS - 4 JF - PLoS Comput Biol SN - 1553-7358 TI - ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun PB - Public Library of Science VL - 1 SP - e43 KW - de-novo KW - repeat AU - Li, Ruiqiang AU - Ye, Jia AU - Li, Songgang AU - Wang, Jing AU - Han, Yujun AU - Ye, Chen AU - Wang, Jian AU - Yang, Huanming AU - Yu, Jun AU - Wong, Gane AU - Wang, Jun PY - 2005/09/23/ UR - http://dx.doi.org/10.1371/journal.pcbi.0010043 ER -