Liu Lei, Gong George, Liu Yong, Natarajan Shreedhar, Larkin Denis M, Everts-van der Wind Annelie, Rebeiz Mark, Beever Jonathan E
The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61801, USA.
Bioinformatics. 2004 Jan 22;20(2):148-54. doi: 10.1093/bioinformatics/bth018.
The completion of human and mouse genome sequences provides a valuable resource for decoding other mammalian genomes. The comparative mapping by annotation and sequence similarity (COMPASS) strategy takes advantage of the resource and has been used in several genome-mapping projects. It uses existing comparative genome maps based on conserved regions to predict map locations of a sequence. An automated multiple-species COMPASS tool can facilitate in the genome sequencing effort and comparative genomics study of other mammalian species.
The prerequisite of COMPASS is a comparative map table between the reference genome and the predicting genome. We have built and collected comparative maps among five species including human, cattle, pig, mouse and rat. Cattle-human and pig-human comparative maps were built based on the positions of orthologous markers and the conserved synteny groups between human and cattle and human and pig genomes, respectively. Mouse-human and rat-human comparative maps were based on the conserved sequence segments between the two genomes. With a match to human genome sequences, the approximate location of a query sequence can be predicted in cattle, pig, mouse and rat genomes based on the position of the match relatively to the orthologous markers or the conserved segments.
The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/
人类和小鼠基因组序列的完成，为解码其他哺乳动物基因组提供了宝贵资源。通过注释和序列相似性进行比较映射（COMPASS）策略利用了这一资源，并已应用于多个基因组映射项目。它利用基于保守区域的现有比较基因组图谱来预测序列的图谱位置。自动化的多物种COMPASS工具可促进其他哺乳动物物种的基因组测序工作和比较基因组学研究。
COMPASS的前提是参考基因组与预测基因组之间的比较图谱表。我们构建并收集了包括人类、牛、猪、小鼠和大鼠在内的五个物种之间的比较图谱。牛-人类和猪-人类比较图谱分别基于直系同源标记的位置以及人类与牛和人类与猪基因组之间的保守同线性群构建。小鼠-人类和大鼠-人类比较图谱基于两个基因组之间的保守序列片段构建。通过与人类基因组序列匹配，可根据匹配相对于直系同源标记或保守片段的位置，预测查询序列在牛、猪、小鼠和大鼠基因组中的大致位置。
COMPASS工具和数据库可在http://titan.biotec.uiuc.edu/COMPASS/获取
