PEDANT server updated

Dmitrij Frishman frishman at mips.biochem.mpg.de
Sat Aug 30 00:23:21 EST 1997


The PEDANT server has been updated. 

Two new genomic sequences have been added:

- Complete genome of H. pylori (special thanks to Dr. A.Kerlavage
  (TIGR) for providing the coding regions prior to publication)
- Plasmid from Rhizobium sp (IMB, Jena)

Your comments and criticisms are welcome.

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PEDANT: Protein Extraction, Description, and ANalysis Tool

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

Features:

- Eight complete and two partial genomic sequences plus one plasmid
analyzed so far:

  S.cerevisiae
  M.genitalium
  M.pneumoniae
  M.jannaschii
  Synechocystis sp.
  H.influenzae
  E.coli
  H.pylori 
  B.subtilis (fragment)
  S.solfataricus (fragment)
  Rhizobium sp.(plasmid) 

- 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  FASTA2 and BLAST2
  similarity searches supplemented by detection of PROSITE
  patterns and motifs and comparisons with conserved sequence 
  blocks

- 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

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




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