PEDANT update: A.aeolicus and signal peptides

[Dmitrij Frishman]

The PEDANT genome analysis server has been updated. 

The genomic sequence of Aquiflex aeolicus has been made available.

For Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes
(yeast) we are now making available predictions of signal peptides made
by the program SignalP (Henrik Nielsen, Jacob Engelbrecht, Sxren Brunak
and Gunnar von Heijne*: Identification of prokaryotic and eukaryotic
signal
peptides and prediction of their cleavage sites. Protein Engineering 10,
1-6
(1997)). Special thanks to Dr. Henrik Nielsen from the Center for
Biological
Sequence Analysis (The Technical University of Denmark) for providing
the
SignalP program and advice on how to use it.

Incorporation of signal peptide predictions has reduced the fraction of 
membrane proteins predicted in each genome by a few percentage points.
Some of the proteins previously predicted to have one transmembrane
region
are now predicted to be globular proteins with a signal peptide in the
N-terminus.

Please note that signal peptide predictions are not available for
Mycobacteria
and Archea.

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:

- 15 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
  A.aeolicus
  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

- 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