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


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 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 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


The UCSC Genome Browser has released an updated mouse genome sequence based on the Feb. 2003 freeze at It includes 705 megabases of finished sequence, compared to 96 Mb in the prior assembly.

Filed under

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.