LOS ANGELES--GeneMine, a popular bioinformatics software package, is being made available free to the academic community. First developed in the early 90’s by Chris Lee, assistant professor at University of California, Los Angeles, when he was a post-doc at Stanford University, GeneMine was one of the first computer tools for retrieving sequence-related information from biological servers on the internet. Originally known as Look, it was for a time the central product of Molecular Applications Group in Palo Alto, Calif., a company that Lee co-founded with Michael Levitt, chair of structural biology at Stanford, in 1993.
With the dissolution of Molecular Applications Group in December, 1999, Lee negotiated to have academic rights to GeneMine transferred to the University of California. Lee told BioInform that he has the right to continue to develop the source code as a free download for all noncommercial users. "Hopefully it will become useful to a lot of researchers out there," he remarked. Commercial rights to the package were acquired by Structural Bioinformatics of San Diego at the same time.
GeneMine’s automated querying services send out sequence and keyword requests to up to 46 biological servers worldwide, such as GenBank, SwissProt, and the Protein Data Bank. Information related to structure, function, disease association, and other important research categories is returned and displayed at the console as sequence-associated annotations. The package also contains a 3-D structure viewer, text processor and alignment editor.
Now in version 3, it’s available at http://www.bioinformatics.ucla.edu/genemine for the three UNIX platforms (SGI’s Irix, Sun’s Solaris, and Linux). A new version, tentatively scheduled for release this summer, will feature a redesigned interface, improved capability for handling large genomic sequence, and expanded access to the new annotation and analysis servers that are proliferating in the bioinformatics universe.