Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Workshop: Comparative Genomics
COMPASS (comparative mapping by annotation and sequence similarity) is a powerful tool for comparative gene mapping in silico. The concept is based upon the extensive conservation of synteny and gene order among mammalian genomes. For two species in which the comparative genome organization is known, the chromosome location of any gene or DNA sequence can be predicted if the sequence is conserved and the map location is known in one of the two species. Our first generation informatics tool demonstrated 95% accuracy of chromosome prediction in the cattle genome (Band et al., Genome Research 10:1359, 2000). Our goal was to develop an enhanced tool that would incorporate data from an ordered radiation hybrid map of the cattle genome thus permitting the predication of location on a chromosome. We have seamlessly integrated the multiple steps of the COMPASS procedure into a web-based interface. These steps are i) identification of putative orthologs by BLASTN search against human UniGene, ii) retrieval of UniGene cluster identification, accession numbers of best hits and other annotation, and iii) prediction of cattle chromosome and bin identification based on a look-up table containing coordinates on an RH-based comparative map of the cattle and human genomes. The new COMPASS II tool provides a significant advancement over the previous version of COMPASS in that RH bin location on the cattle map can be accurately predicted. Furthermore, the tool can be extended to any other species that has adequate RH mapping information. A web-tool for single-sequence prediction is available to the public at: http://keck1.biotec.uiuc.edu:8887/example/servlets/mainpage/html.