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Thursday, March 02, 2000

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CCP11 Newsletter Issue 10
InterPro – An integrated documentation resource for protein families, domains and functional sites
"InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects."

PIX - Protein Identification Application
"PIX a World Wide Web based tool to view the results of running many protein analysis programs on your peptide sequence."

The TIGR Gene Indices: A Resource to Estimate the Transcript Content of Genomes
"The TIGR Gene Indices (TGI) represent a best guess of transcript content in the genomes of ten plant and animal species through the meticulous cataloguing of Expressed Sequence Tags (ESTs) and coding sequences, which are downloaded from Genbank on a continual basis. The TGI species include human, rat, mouse, Drosophila, zebrafish, Arabidopsis, Maize, Rice, Soybean, and Tomato. An eleventh index for potato is planned for introduction in 2000."

ChiMap (Change in Intensity of Multiple Associated Proteomes) program to enable easy identification of significant expression changes in a series of 2D gels.
"Analysis of the cellular proteome involves the characterization, analysis and subsequent identification of thousands of proteins. As two-dimensional gel electrophoresis technology improves it will be possible to characterize better and therefore visualize a larger percentage of the total protein complement. The total cellular protein complement has been estimated as 20,000 separate proteins, many of which will have several post translational modifications. With the steady increase in information on a 2D gel it becomes imperative to develop a set of user-friendly tools to identify features that are interesting for identification by mass spectrometry in addition to enable the tracking of changes in protein expression over a set of defined parameters such as substrate-activation or simply time."

The Power of Patent Information
"Since its launch in 1990, Derwent’s GENESEQ database has rapidly become the world’s largest database exclusively devoted to nucleic acid and amino acid sequences from patents. In 1998, GENESEQ was launched in flat file (ASCII text) EMBL format which enables integration of the database into in-house bioinformatics systems. It is a unique information resource, which allows professional searchers to identify patents containing a given sequence, or a sequence substantially homologous with it, in a single operation.

All patents containing nucleic acid or amino acid sequence information are analysed and any new nucleotide sequences of 10 or more bases, protein sequences of 4 or more amino acids and new primers and probes are added to the database. To date, the database contains over 600,000 records from 40 patent-issuing authorities, including US and PCT. Of the records, some 20% are from foreign language patents from countries including Japan, Germany, France, Latin America, Russia, Korea, China and Hungary, among others.

GENESEQ is updated every two weeks, with about 2,000-3,000 new records added at each update."

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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