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UCSC genome browser, Ensembl, GenBank, SRS, DiscoveryLink, NCBI web services, SSAHA 3.1, SuMo


Concurrent with last week’s announcement of the completion of the Human Genome Project, both the UCSC genome browser and Ensembl released versions of the latest assembly (NCBI build 33). UCSC is providing bulk downloads of the data via ftp at or through the genome browser downloads link at downloads.html. Ensembl is providing the data at


GenBank release 135.0 is now available from NCBI at The release contains 31,099,264,455 base pairs and 24,027,936 entries, up by 1.7 million base pairs and 992,113 sequence records from the February 134.0 release. Uncompressed, the 135.0 flat files require about 100 GB for the sequence files only. The ASN.1 version requires around 89.67 GB. As of the April 14 announcement of the completion of the HGP, GenBank contained 9,743,398,611 base pairs of human sequence, and 6,574,171 human sequence records.


Lion Bioscience has released a new software wrapper that integrates SRS with IBM’s DiscoveryLink middleware. The wrapper will enable users to write SQL queries to access SRS, while DiscoveryLink customers will be able to use SRS to integrate either flat- file or relational biological databases.


Lion has also released version 3.2 of its Lion DiscoveryCenter integration platform, which integrates chemical compound databases from MDL Information Systems as well as in-house customer databases using MDL’s Relational Chemistry Server data cartridge.


IBM is offering a free trial download of a suite of web services technology for the NCBI databases, including wrappers for GenBank, PubMed, and Blast, at


SSAHA 3.1 is available at The release addresses several platform compatibility issues.


SuMo, a web-based system for finding structural similarities in 3D structures of proteins is available from Pôle Bio-Informatique Lyonnais at


Filed under

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.