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PEP: Predictions for Entire Proteomes


NAR Molecular Biology Database Collection entry number 377
Carter, P.1, Liu, J.2, Rost, B.1
1Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
2Department of Pharmacology, Columbia University, 630 West 168th Street, New York, NY 10032, USA

Database Description

PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes, and archaea. All proteins publicly available for each organism were aligned against SWISS-PROT, TrEMBL and PDB. Additionally the following annotations are provided: secondary structure, transmembrane helices, coiled coils, regions of low complexity, signal peptides, nuclear localization signals, PROSITE motifs and classes of cellular function. Proteins that contain long regions without regular secondary structure are also identified. We have produced a related database of structural domain-like fragments derived from PEP, and clusters based on homology between all fragments. The PEP database, fragments and clusters are distributed freely as a set of flat files, and have been integrated into SRS. The PEP group of databases can be accessed from: http://cubic.bioc.columbia.edu/pep.

Acknowledgements

Thanks to Dariusz Przybylski, Rajesh Nair and Kazimierz Wrzeszczynski (Columbia University) for providing preliminary information and programs. Thanks to the SRS team for their software. The work was supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH). Last, not least, thanks to all those who deposit their experimental data in public databases, and to those who maintain these databases.

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