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PEDANT -- analysis of complete genomes
Introduction
PEDANT stands for Protein Extraction, Description, and ANalysis Tool and is a software system for completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes. It features:
- Seven complete and two partial genomic sequences analysed 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
Information provided by: Dmitrij Frishman
Resources and further information
Max-Planck-Institute for Biochemistry/GSF (German only)
http://www.biochem.mpg.de/
Munich Information Centre for Protein sequences (MIPS)
http://www.mips.biochem.mpg.de/
PEDANT WWW server
http://pedant.mips.biochem.mpg.de/
External sites are not endorsed by EMBL-EBI |
