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Geospiza Finch Genotyping Data Manager, StackPack, GeneSifter, Metabolic Vision, Protein Biomarker, GeneMarker, UCSF Genome Browser and Blat server


Geospiza has released the Geospiza Finch Genotyping Data Manager, an add-on component to the Geospiza Finch Sequencing Center software designed to help manage and analyze genotyping data from ABI’s capillary instruments. Geospiza also launched version 2.12 of the Geospiza Finch Sequencing Center platform. Pricing for the Finch Genotyping Data Manager ranges from $4,995 to $9,995.

Electric Genetics has released a new version of its StackPack transcript management system that is compatible with a new EST clustering method called WCD and a new cluster analysis tool termed SCAT.

VizX Labs has released version 2004.3 of its GeneSifter microarray analysis software, which includes several new features of interest to Affymetrix users, including direct access to CHP and CEL data files. Additional information is available at

Integrated Genomics and Ariadne Genomics have launched Metabolic Vision, a microbial metabolic pathway database that combines Ariadne’s PathwayAssist’s pathway analysis software with Integrated Genomics’ ERGO database of more than 600 curated genomes. The database is available as a module for PathwayAssist customers.

Predictive Patterns Software has released a Protein Biomarker package that is installed on top of its GeneLinker Gold and Platinum 4.5 software. The module allows import and analysis of mass spectrometry data, and works with a number of platforms, including Ciphergen ProteinChip and Advion’s Nanomate, the company said. Predictive Patterns is offering the proteomics analysis package free to its current GeneLinker customers.

SoftGenetics has released GeneMarker, a genotyping software package for amplified fragment-length polymorphism (AFLP), fragment, STR, and microsatellite analysis. GeneMarker is designed for Windows, and can analyze up to 1,000 lanes of data generated by either slab gel or capillary, the company said. GeneMarker is available for academic institutions at $2,000 for a single user license, and $8,000 for a site license for up to 10 concurrent users. The company did not provide pricing information for commercial users.

The University of California Santa Cruz Genome Bioinformatics Group has released a Genome Browser and Blat server for the latest human genome reference sequence (NCBI Build 35, May 2004). Bulk downloads of the data are available at or through the Genome Browser downloads page ( UCSC also released a Genome Browser and Blat server for a second species of fruitfly, Drosophila yakuba.


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The Scan

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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.