TY - JOUR
T1 - PEP
T2 - Predictions for entire proteomes
AU - Carter, Phil
AU - Liu, Jinfeng
AU - Rost, Burkhard
N1 - Funding Information:
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 Institutes 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.
PY - 2003/1/1
Y1 - 2003/1/1
N2 - 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 organisms 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, PROSITE motifs, nuclear localization signals 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.
AB - 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 organisms 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, PROSITE motifs, nuclear localization signals 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.
UR - http://www.scopus.com/inward/record.url?scp=0037250635&partnerID=8YFLogxK
U2 - 10.1093/nar/gkg102
DO - 10.1093/nar/gkg102
M3 - Review article
C2 - 12520036
AN - SCOPUS:0037250635
SN - 0305-1048
VL - 31
SP - 410
EP - 413
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 1
ER -