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Compass, SwissProt, Trembl, PCTGEN, EcoCyc, MetaCyc, Pathway Tools, UCSC Genome Browser

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Bruker Daltonics has released Compass, a software environment that includes instrument control and data processing for mass spectrometry, along with chemoinformatics and bioinformatics analysis modules that include Biotools for protein sequence confirmation, RapiDeNovo for sequencing of peptides, MetaboliteTools for advanced comparison of LC/MS datasets, and LibrarySearch for comparison of MS/MS spectra against reference spectra.

 

Version 41.0 of SwissProt is now available from the EBI at www.ebi.ac.uk/sprot/. The release contains 122,564 fully annotated sequences, and 44,986,459 amino acids. Release 23.0 of Trembl is also available. It contains 921,952 entries and 40,914,860 amino acids.

 

FIZ Karlsruhe and STN International have launched a new nucleotide and amino acid sequence database called PCTGEN that contains sequence and patent application information submitted electronically to the World Intellectual Property Organization. The database currently contains around 1.5 million records. Further information is available at www.stn-international.de/stndatabases/ databases/pctgen.html.

 

SRI has released version 7.0 of the EcoCyc E. coli model organism database, the MetaCyc metabolic pathway database, pathway/ genome databases for 13 additional organisms, and the Pathway Tools software used to query and visualize the databases. In addition, a new Linux port of Pathway Tools is now available. The databases and tools are all available at BioCyc.org.

 

The UCSC Genome Browser has released an updated mouse genome sequence based on the Feb. 2003 freeze at http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm3. It includes 705 megabases of finished sequence, compared to 96 Mb in the prior assembly.

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The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.