MULTI-SPECIES COMPARATIVE MAPPING IN SILICO USING THE COMPASS STRATEGY

¹ The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, 1201 W. Gregory Dr., Urbana, Illinois 61801, USA

² Department of Animal Sciences, 1201 W. Gregory Dr., Urbana, Illinois 61801, USA

³ Biophysics and Computational Biology Program, 607 South Mathews Ave. Urbana, Illinois 61801, USA

The completion of human and mouse genomes sequences provides a valuable resource for decoding other mammalian genomes. The comparative mapping by annotation and sequence similarity (COMPASS) strategy has been used in several genome mapping and sequencing projects including cattle and pig. An automated and web accessible COMPASS tool for multiple species can facilitate in the genome sequencing and mapping effort. In this paper, a COMPASS tool is presented that can make in silico map prediction on both cattle and pig genome maps using human and mouse genome sequence as a common reference. The prerequisite of the COMPASS-tool are cattle-human and pig-human comparative map tables, which are based on the positions of orthologous markers in human genome sequence and cattle or pig genome maps. A pig-human comparative map table was built with more than 600 shared orthologous gene markers (Type I) and a cattle-human comparative map table with more than 700 shared orthologous Type I markers. The two tables are indexed by human chromosomes and their corresponding base pair coordinates. The first step of the COMPASS strategy is to find similar sequences in the human genome using BLASTN. Based on the base pair coordinates of the hit, the closest marker on the human chromosome that is also placed on the cattle or pig map can be found. Using the comparative mapping table, the approximate location of the query sequence in the cattle or pig map can be predicted. The COMPASS-tool is available at: http://keck1.biotec.uiuc.edu:8887/examples/servlets/mainpage.html.