Announce: protein annotations

Arne Mueller a.mueller at icrf.icnet.uk
Mon Nov 12 05:07:25 EST 2001

Dear All,

I'd like to announce our new web resource
http://www.bmm.icnet.uk/3dgenomics/ which provides protein annotation
for fully sequenced genomes. The database has a focus on protein
structure (SCOP doamins). These are the main features:

- general overview of the annotation status of a particular genome
- assignment of SCOP superfamilies to genomes
- comparison of occurence and frequencies of SCOP superfamilies in
different genomes
- SCOP superfamilies in globular parts of membrane proteins in different
- PFAM, SwissProt, PIR assignments + text search of annotation
- annotation of protein from human disease genes
- a detaild report for each processed protein sequence, including:
	- prediction of transmembrane, coiled-coil and low complexity regions
        - signal peptides
        - SCOP, PFAM, PDB, SwissProt+PIR assignments
        - Prosite pattern matches
        - detection of internal repeats
        - Position Specific Sequence Profiles (from PSI-BLAST)
        - secondary structure prediction
        - search for homologous sequences using BLAST, PSI-BLAST, IMPALA
or 3D-PSSM and
          filter the restuls for one ore more taxonomic groups, source
databases or genomes
        - access alignments (mutiple alignnment style or pairwise
        - sequence searches + alignments are precompiled and easy to
access (I hope ;-)

The web-site is a side-product of ongoing research projects in our lab,
but it's free to access. The web-resource is still under construction
and may change in future. In particular we try to speed things up. Just
give it a try ...



Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | fax :+44-(0)171-269-3534
email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk

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