Abstract One of the challenges to the effective utilization of cDNA microarray analysis in mouse models of oncogenesis is the choice of a critical set of probes that are informative for human disease. Given the thousands of genes with a potential role in human oncogenesis and the hundreds of thousands of mouse sequences available for use as probes, selection of an informative set of mouse probes can be an overwhelming task. We have developed a web based sequence mining tool using DataBase Independent (DBI) Perl to annotate publicly available sequences. The Mouse Oncochip Design Tool uses the Mouse Genome Database (MGD) developed and maintained by the Jackson Laboratories for mouse DNA sequences. There are over 380 000 sequences in their database. The output list has been ordered to present the genes more likely to be informative in a mouse model of human cancer using a candidate set of oncogenes to order the list. Mouse sequences that represent genes that are homologous with a member of a human oncogene set are listed first. In addition it provides a set of links for information on clone source gene function. Contact: http://nciarray.nci.nih.gov/cgi-bin/me/mouse_design.cgi * To whom correspondence should be addressed. 5 Current address: Department of Pathology and Biomedical Informatics, Vanderbilt University Medical Center, MCN C-3321, Nashville TN 37232, USA. 6 Current address: Department of Pharmacology, School of Medicine, University of Colorado Health Sciences Center, 4200 E Ninth Avenue, Denver CO 80262, USA. 7 Current address: Genome Institute of Singapore, 1 Research Link, IMA Building #04-01, National University of Singapore, Singapore 117604.