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PEDANT update: experimental and unfinished genomes

Dmitrij Frishman frishman at mips.biochem.mpg.de
Tue May 19 02:58:23 EST 1998


The PEDANT genome analysis server has been updated. 

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

Several experimental and unfinished genomic sequences have been 
made available:

- Saccharomyces pombe (fragment) (The Sanger Center)
- Mycobacterium tuberculosis (The Sanger Center)
- Deinococcus radiodurans (TIGR)
- Streptococcus pneumoniae (TIGR)
- Rhodobacter capsulatus (fragment) (Chicago University)

Special thanks to Valerie Wood (The Sanger Centre) for providing 
the S. pombe protein coding regions and Michael Fonstein (Chicago
University) for making available the partial R.capsulatus sequence.

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:

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

  S.cerevisiae
  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 (fragment)
  M.tuberculosis 
  D.radiodurans 
  S.pneumoniae 
  R.capsulatus (fragment)

- 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

- Signal peptide predictions

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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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