PEDANT: Automatic Genome Analysis

Dmitrij Frishman frishman at mips.biochem.mpg.de
Mon Jun 2 11:07:36 EST 1997


Dear colleagues,

we are pleased to announce the availability of a new WWW
server devoted to computational analysis of complete genomes.

----------------------------------------------------------------

PEDANT: Protein Extraction, Description, and ANalysis Tool

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

Features:

- Seven complete and two partial genomic sequences analyzed so far:

  S.cerevisiae
  M.genitalium
  M.pneumoniae
  M.jannaschii
  Synechocystis sp.
  H.influenzae
  E.coli
  B.subtilis (fragment)
  S.solfataricus (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
  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

----------------------------------------------------------------

Dmitrij Frishman and Hans-Werner Mewes
Munich Information Centre for Protein sequences
Max-Planck-Institut f. Biochemie/GSF
http://www.mips.biochem.mpg.de




More information about the Bionews mailing list