reas recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun意图复苏的祖先的转座因子序列未装配的读取整个基因组的猎枪.pdfVIP

ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun 1,2[ 1,2[ 2,3[ 2[ 2 2 1,2 1,2 Ruiqiang Li , Jia Ye , Songgang Li , Jing Wang , Yujun Han , Chen Ye , Jian Wang , Huanming Yang , 1,2 1,2,4* 1,2,5,6* Jun Yu , Gane Ka-Shu Wong , Jun Wang 1 James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou, China, 2 Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing, China, 3 College of Life Sciences, Peking University, Beijing, China, 4 UW Genome Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America, 5 The Institute of Human Genetics, University of Aarhus, Aarhus, Denmark, 6 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark 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. Citation: Li R, Ye J, Li S, Wang J, Han Y, et al (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4): e43. Introduction