Multi-species comparative mapping in silico using the COMPASS strategy.
BACKGROUND
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.


BACKGROUND
The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/
Liu
Lei
L
The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61801, USA. leiliu@uiuc.edu
Gong
George
G
Liu
Yong
Y
Natarajan
Shreedhar
S
Larkin
Denis M
DM
Everts-van der Wind
Annelie
A
Rebeiz
Mark
M
Beever
Jonathan E
JE
D000465:Algorithms; D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D005819:Genetic Markers / Q000235:genetics*; D006801:Humans; D051379:Mice; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity
D005819:Genetic Markers