Laura Elnitski1,2, Belinda Giardine1, Cathy Riemer1, Izabela Makalowska3, Webb Miller1,4, and Ross Hardison2Departments of Computer Science and Engineering1, Biochemistry and Molecular Biology2 and Biology5 and Life Sciences Consortium3 at Penn State University
Genome browsers provide sequences, comprehensive annotations and alignments with other genome sequences. These are essential resources to the genomics community. However, the querying capacity is usually limited to information contained within a single track (e.g. SNPs or genes), with no opportunity for querying across various tracks.
We have developed a database that combines data from the Human Genome Browser, Ensembl, LocusLink and other sources, along with human-mouse sequence alignments. The query interface allows users to find desired information from a wide variety of resources in a convenient and intuitive fashion. For example, one can find "all conserved noncoding sequences with greater than 70% identity for at least 100 bp that appear within 1000 bp of the 5' end of genes encoding zinc finger proteins". Queries can incorporate additional information such as expression levels and disease association data. A "history page" allows earlier queries to be retrieved, modified, and combined as desired, to facilitate construction of even more sophisticated queries. Addition of more information is planned, such as transcription factor binding sites.
The current version of this database supports queries on chromosome 22, due to the extensive amount of annotation available for this chromosome. Future development may expand the database to include other chromosomes.
Home page
Menu