bioinformatics advance access published june 24, 2004 the unimarker (um) method for synteny推荐.pdf

Bioinformatics Advance Access published June 24, 2004 Bioinformatics © Oxford University Press 2004; all rights reserved. The UniMarker (UM) Method for Synteny Mapping of Large Genomes 1,4 2,3,4 2 1,* Liao, Ben-Yang, Yu-Jung Chang, Jan-Ming Ho , and Ming-Jing Hwang 1 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 2 Institute of Information Science, Academia Sinica, Taipei, Taiwan 3 Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan 4 These authors contributed equally to this work. Running title: Synteny Mapping using UniMarkers * To whom correspondence should be addressed Ming-Jing Hwang, Ph.D. Institute of Biomedical Sciences Academia Sinica 128 Yen-Chiou Yuan Rd., Sec. 2 Taipei 11529 Taiwan Tel: +886-2-2789-9033 Fax: +886-2-2788-7641 Email: mjhwang@.tw 1 ABSTRACT Motivation: Synteny mapping, or detecting regions that are orthologous between two genomes, is a key step in studies of comparative genomics. For completely sequenced genomes, this is increasingly accomplished by whole-genome sequence alignment. However, such methods are computationally expensive, especially for large genomes, and require rather complicated post-processing procedures to filter out non-orthologous sequence matches. Results: We have developed a novel method that does not require sequence alignment for synteny mapping of two large genomes, such as the human and mouse. In this method, the occurrence spectra of genome-wide unique 16-mer sequences present in both the human and mouse genome are used to directly detect orthologous genomic segments. Being sequence alignment-free, the method is very fast and able to map the two mammalian genomes in one day of com