PEDANT update

Petra Maierl maierlp at mips.biochem.mpg.de
Wed Jan 7 07:14:51 EST 1998


The PEDANT genome analysis server has been updated. 

Three new genomic sequences have been added:

- M.thermoautotrophicum
- A.fulgidus 
- B.burgdorferi

The Bacillus subtilis genome is now complete.

The following genomes have been updated:

- S.cerevisiae
- M.genitalium
- M.pneumoniae
- M.jannaschii
- Synechocystis sp.
- H.influenzae
- E.coli

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:

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

  S.cerevisiae
  M.genitalium  M.jannaschii
  Synechocystis sp.
  H.influenzae
  E.coli
  H.pylori 
  B.subtilis
  M.thermoautotrophicum
  A.fulgidus 
  B.burgdorferi
  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
  M.pneumoniae




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