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Vol. 20 no. 2 2004, pages 148-154
Bioinformatics © Oxford University Press 2004; all rights reserved.

PAG Meeting Original Paper

Multi-species comparative mapping in silico using the COMPASS strategy

Lei Liu 1,2,*, George Gong 1, Yong Liu 1, Shreedhar Natarajan 3, Denis M. Larkin 2, Annelie Everts-van der Wind 2, Mark Rebeiz 2 and Jonathan E. Beever 2

1 The W. M. Keck Center for Comparative and Functional Genomics, 2 Department of Animal Sciences and 3 Biophysics and Computational Biology Program, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61801, USA

Received on November 9, 2003 ; accepted on November 11, 2003

Motivation: 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.

Results: 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.

Availability: The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/

Contact: leiliu{at}uiuc.edu

* To whom correspondence should be addressed.


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