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Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2007 35(Database issue):D241-D246; doi:10.1093/nar/gkl850
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Nucleic Acids Research, 2007, Vol. 35, Database issue D241-D246
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

EVEREST: a collection of evolutionary conserved protein domains

Elon Portugaly*, Nathan Linial and Michal Linial1

School of Computer Science & Engineering, Institute of Life Sciences The Hebrew University of Jerusalem 1 Department of Biological Chemistry, Institute of Life Sciences The Hebrew University of Jerusalem

*To whom correspondence should be addressed. Email: elonp{at}cs.huji.ac.il

Received August 15, 2006. Revised October 9, 2006. Accepted October 9, 2006.

Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatics, 7, 277, is one such system that performs the task automatically, using protein sequence alone. Herein we describe EVEREST release 2.0, consisting of 20 029 families, each defined by one or more HMMs. The current EVEREST database was constructed by scanning UniProt 8.1 and all PDB sequences (total over 3 000 000 sequences) with each of the EVEREST families. EVEREST annotates 64% of all sequences, and covers 59% of all residues. EVEREST is available at http://www.everest.cs.huji.ac.il/. The website provides annotations given by SCOP, CATH, Pfam A and EVEREST. It allows for browsing through the families of each of those sources, graphically visualizing the domain organization of the proteins in the family. The website also provides access to analyzes of relationships between domain families, within and across domain definition systems. Users can upload sequences for analysis by the set of EVEREST families. Finally an advanced search form allows querying for families matching criteria regarding novelty, phylogenetic composition and more.

Minor amendments have been made to the text and Table 1


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