Skip to main content
Premium Trial:

Request an Annual Quote

Russian Startup Licenses Database to Biomax

NEW YORK, April 2 – Bioinformatics startup Softberry of Novosibirsk, Russia and White Plains, NY, said Monday it had licensed its human genome database to Biomax of Martinsried, Germany.

Valery Sagitov, president of Softberry, told GenomeWeb that the database contains predicted gene sequences as well as protein homologies.

To create the database, Softberry used its gene prediction programs to predict gene sequences in public databases and then ran those sequences against public protein databases in order to find homologies.

Software developer Biomax, which has the exclusive license to sell subscriptions to the database, intends to further develop and annotate the database using its Pedant-Pro Sequence Analysis Suite to create the Pedant Human Genome Database.

“The exclusive Fgenesh++ Softberry software is one of the most powerful systems for gene prediction available and gives substantially more accurate predictions than other commonly used approaches,” said Klaus Heumann, CEO of Biomax.

“Softberry gene prediction programs can produce ab initio annotation of the whole human genome in several hours, which is important for producing updated versions of the database using improved sequences of human genome,” Heumann said.

Sagitov said that Softberry’s prediction tools are fully automatic, allowing for faster and more accurate gene prediction.

“In 40 hours we can do the full annotation of the human,” said Sagitov, who attributed the company’s computational ability to the scientific founders’ 20 plus years doing gene prediction in academic settings in Russia.

Softberry, which was founded less than a year ago, has seven employees in Russia and two in New York.

The company has 40 licensees for its gene prediction software, including Celera, Merck, Incyte, Amgen, and Bristol-Myers Squibb. Licenses generally cost between $10,000-$15,000 per year, per site.

Softberry’s proprietary Fgenesh++ script uses sequences of human chromosomes, alignment software, and the company’s own gene prediction programs, Fgenesh and Fgenesh+, to identify human genes.

In addition, to its gene prediction programs Softberry has also developed genome comparison tools DBSCAN and Scan2, protein sub-cellular localization predictor ProtComp, expression analysis program Seltarget, RNAmap and Oligomap programs for RNA/EST/oligo mapping to chromosome sequences, and the Genome Information Viewer.

Softberry has raised several hundred thousand dollars in venture capital to date.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.