Skip to main content

Molecular Applications Group s GeneMine Now Available at No Cost to Academics



OS 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 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.

--Potter Wickware

Filed under

The Scan

Rise of B.1.617.2 in the UK

According to the Guardian, UK officials expect the B.1.617.2 variant to soon be the dominant version of SARS-CoV-2 there.

Anne Schuchat to Retire

Anne Schuchat is retiring after more than 30 years at the US Centers for Disease Control and Prevention, Politico reports.

US to Share More Vaccines

CNN reports that the US will share 20 million doses of the Moderna, Pfizer, and Johnson & Johnson SARS-CoV-2 vaccines with other countries.

PNAS Papers on Gene Therapy Platform, Aspergillus Metabolome, Undernutrition Model Microbiome

In PNAS this week: approach to deliver protein-based treatments to cells, pan-secondary metabolome of Aspergillus, and more.