PEDANT update: M.tuberculosis and 8 unfinished genomes

Dmitrij Frishman frishman at mips.biochem.mpg.de
Mon Jun 29 03:46:43 EST 1998


The PEDANT genome analysis server has been updated. 

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

The complete genomic sequence of Mycobacterium tuberculosis released by 
the Sanger Centre has been analysed.

Several new experimental and unfinished genomic sequences have been 
made available:

- Neisseria meningitidis (Sanger Centre)
- Chlamydia trachomatis (University of California at Berkeley and
  Stanford University)
- Clostridium acetobutylicum (Genome Therapeutics Corporation)
- Mycobacterium leprae (Sanger Centre)
- Streptomyces coelicolor (Sanger Centre)
- Pseudomonas aeruginosa (PathoGenesis Corporation)
- Enterococcus faecalis (The Institute for Genetic Research)
- Campylobacter jejuni (Sanger Centre) 

The following computational methods have been added:

- HMMER
    Hidden Markov model software for sensitive searches against a
    database of protein domains.
    Sonnhammer E.L.L., Eddy S.R., Durbin R. (1997) Pfam: A 
    Comprehensive Database of Protein Families Based on
    Seed Alignments. Proteins 28, 405-420. 

- pI 
    Perl script that returns the amino acid composition, molecular
    weight, theoretical pI, and expected extinction
    coefficient of an amino acid sequence.
    By Fred Lindberg. 


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:

- 28 complete and 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 
  M.tuberculosis 
  D.radiodurans 
  S.pneumoniae 
  R.capsulatus (fragment)
  C.jejuni
  N.meningitidis 
  C.trachomatis 
  C.acetobutylicum 
  M.leprae 
  S.coelicolor 
  P.aeruginosa 
  E.faecalis 

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

- 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

- Molecular weight and pI

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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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