PEDANT update: T.pallidum

[Dmitrij Frishman]

The PEDANT genome analysis server has been updated. 

The genomic sequence of Treponema pallidum has been made available.

Please note that the analysis is based on the PRELIMINARY set of peptide
sequences released
by the T. pallidum Molecular Genetics Group at the University of Texas.

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:

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