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