The PEDANT genome analysis server has been updated.
http://pedant.mips.biochem.mpg.de/frishman/pedant.html
Several experimental and unfinished genomic sequences have been
made available:
- Saccharomyces pombe (fragment) (The Sanger Center)
- Mycobacterium tuberculosis (The Sanger Center)
- Deinococcus radiodurans (TIGR)
- Streptococcus pneumoniae (TIGR)
- Rhodobacter capsulatus (fragment) (Chicago University)
Special thanks to Valerie Wood (The Sanger Centre) for providing
the S. pombe protein coding regions and Michael Fonstein (Chicago
University) for making available the partial R.capsulatus sequence.
Your comments and criticisms are welcome.
----------------------------------------------------------------
PEDANT: Protein Extraction, Description, and ANalysis Tool
http://pedant.mips.biochem.mpg.de/frishman/pedant.html
Features:
- 18 complete and two 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 (fragment)
M.tuberculosis
D.radiodurans
S.pneumoniae
R.capsulatus (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 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
----------------------------------------------------------------
Dmitrij Frishman, Petra Maierl, and Hans-Werner Mewes
Munich Information Centre for Protein sequences/GSF
http://www.mips.biochem.mpg.de
