[Announce] Automatic analysis of a cyanobacterial genome

Sebastian Hoersch hoersch at ebi.ac.uk
Tue Oct 28 05:20:52 EST 1997


AUTOMATIC ANALYSIS OF THE FULL SET OF SYNECHOCYSTIS SP. PROTEINS

              http://www.sander.ebi.ac.uk/genequiz


The amino acid sequences of 3168 open reading frames [ORFs] of this
photoautotrophic bacterium [1] were analyzed at EMBL-EBI using a new
version of the GeneQuiz software system. For an example of one ORF, try:
http://columba.ebi.ac.uk:8765/gq/gq_report?project=CY97a&orf=sll1758

Results include information about more than 350 ORFs originally
annotated as hypothetical for which GeneQuiz found functional annotation
derived by putative homology.

GeneQuiz performs large scale automatic analyses of protein sequences by
integrating the results of a range of methods under a reasoning module
that
extracts functional annotation.

A web-based user interface provides access to the results together with
supporting evidence in the form of a hyperlinked report for each
sequence,
including:

- suggested functional annotation,
- list of putative homologs [2],
- multiple sequence alignments,
- links to entries in primary sequence and motif databases [3],
- links to the raw output of the underlying sequence analysis tools,
- predicted secondary structure for many ORFs [4],
- 3D structures modelled by homology [5].

Releases of functional annotation for other completely sequenced genomes
are planned.


Acknowledgements:

[1] Sequences provided by the Kazusa DNA Research Institute, Japan: 
http://dnap1.kazusa.or.jp/cyano/

[2] Information for this analysis was derived using the following
sequence
and pattern databases: swissprot/swissnew, pir, trembl/tremblnew,
genpept/
genpeptnew, embl/emnew, genbank, pdb, worm and prosite.

[3] SRS (Sequence Retrieval System, Etzold et al.):
http://srs.ebi.ac.uk:5000/

[4] PHD (Rost et al.):
http://www.embl-heidelberg.de/predictprotein/predictprotein.html

[5] WHATIF (Vriend et al.):
http://swift.embl-heidelberg.de/whatif/index.html


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Sebastian Hoersch, Christophe Leroy, Nigel Brown, Miguel Andrade,
Angelo Franchini, Christian Reich, Chris Sander

European Bioinformatics Institute (EMBL-EBI)

Contact: genequiz at embl-ebi.ac.uk
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