PEDANT: update and address change

Dmitrij Frishman frishman at mips.biochem.mpg.de
Wed Sep 9 04:32:48 EST 1998


The PEDANT genome analysis server has been updated. Please note the new
address:

http://pedant.mips.biochem.mpg.de/

The FCA contig of the A.thaliana genome (Bevan M, et al. Nature. 1998
Jan 29;
391(6666): 485-488.) is now available.

The partial S.pombe genomic sequence has been updated in collaboration
with Dr. Valerie Wood (Sanger Center).

Five new unfinished genomic sequences have been analyzed:

-Pyrococcus furiosus (University of Utah Genome Center)
-Neisseria gonorrhoeae (University of Oklahoma's Advanced 
	Center for Genome Technology)
-Streptococcus pyogenes (University of Oklahoma's Advanced
	Center for Genome Technology)
-Actinobacillus actinomycetemcomitans (University of Oklahoma's
	Advanced Center for Genome Technology)
-Yersinia pestis (Sanger Center in collaboration with the 
	Department of Medical Microbiology, St. Bartholomew's
	and The Royal London School of Medicine and Dentistry,
	Queen Mary and Westfield College, London)

Your comments and criticisms are welcome. 

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PEDANT: Protein Extraction, Description, and ANalysis Tool

http://pedant.mips.biochem.mpg.de/

Features:

- 35 complete and partial genomes plus one plasmid analyzed so far:

  S.cerevisiae
  A.thaliana
  M.genitalium
  M.pneumoniae
  M.jannaschii
  Synechocystis sp.
  H.influenzae
  E.coli
  H.pylori 
  B.subtilis
  M.thermoautotrophicum
  A.fulgidus 
  B.burgdorferi
  P.horikoshii OT3
  T.pallidum
  A.aeolicus
  Rhizobium sp. (plasmid) 
  S.pombe 
  M.tuberculosis 
  D.radiodurans 
  S.pneumoniae 
  R.capsulatus (fragment)
  C.jejuni
  N.meningitidis 
  C.trachomatis 
  C.acetobutylicum 
  M.leprae 
  S.coelicolor 
  P.aeruginosa 
  E.faecalis 
  P.furiosus 
  N.gonorrhoeae 
  S.pyogenes 
  A.actinomycetemcomitans 
  Y.pestis

- Exhaustive functional and structural classification of
  the predicted open reading frames from fully sequenced
  genomes using a combination of sequence comparison and
  prediction techniques

- Functional assignment of ORFs on the basis of BLAST2
  similarity searches supplemented by detection of PROSITE
  patterns and motifs and comparisons with conserved sequence 
  blocks and protein domains

- Automatic attribution of sequences with significantly related
  PIR entries to one of the PIR super-families

- Functional classification of gene products through similarity
  searches against several curated master gene sets from 
  bacteria and yeast with manually assigned functional classes

- Extraction of available 3D information through Smith-Waterman
  similarity comparisons of every sequence with the STRIDE 
  database of secondary structure assignments

- Secondary structure and transmembrane region predictions

- Detection of low-complexity and coiled coil regions

- Signal peptide predictions

- Molecular weight and pI

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Dmitrij Frishman, Petra Maierl, and Hans-Werner Mewes
Munich Information Centre for Protein sequences/GSF
http://www.mips.biochem.mpg.de



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