PEDANT update

Dmitrij Frishman frishman at mips.biochem.mpg.de
Wed Nov 4 04:15:19 EST 1998


The PEDANT genome analysis server has been updated.

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

The complete Chlamydia trachomatis genome (University of California,
Berkeley)
has been added.

Four new unfinished genomic sequences have been analyzed:

- Chlorobium tepidum (The Institute of Genomic Research)
- Vibrio cholerae (The Institute of Genomic Research)
- Clostridium acetobutylicum (Genome Therapeutics Corporation)
- Bordetella pertussis (Sanger Centre)

Your comments and criticisms are welcome. 

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PEDANT: Protein Extraction, Description, and ANalysis Tool

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

Features:

- 38 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
  C.tepidum
  V.cholerae
  C.acetobutylicum
  B.pertussis

- 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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