NCBI Home Genomic Biology Mouse Genome ResourcesTutorial Search Entrez NCBI Web Site ------------- Books Domains 3D Domains Gene Genome GEO GEO Datasets HomoloGene Journals LocusLink Map Viewer MeSH Nucleotide OMIM PMC PopSet Protein PubMed SNP Structure Taxonomy UniGene UniSTS

2. For a given region of the mouse genome, how can I use comparative genomics to inform by gene identification project?

A. HomoloGene
HomoloGene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene) is a comparative genomics resource that performs reciprocal best hit analysis of protein products from completely sequenced genomes. A very conservative approach is used to identify potential orthologs. You can perform a Gene Centric search [try Cftr] or an organism centric search [try mouse [orgn] to find mouse specific clusters or mouse [orgn] human [orgn] to find proteins conserved in human and mouse).

B. Comparative Map Viewer
We import HomoloGene data into the Map Viewer. Genes with an HomoloGene link will have an 'hm' linkout on the Genes_seq map. We also use this information to calculate conserved synteny bins (although it is clear we need to refine this algorithm). We will start out looking at a 15 Mb region on Mmu6 encompassing the Cftr gene. Using the Maps & Options window, we can select the organism of interest (in this case human) and add any human maps we wish to see. In cases where alternate assemblies are available for a given organism the comparative view is available only for the reference assemblies.