Skip Navigation



Nucleic Acids Research Advance Access published online on November 11, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl850
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (677K) Freely available
Right arrow Screen PDF (205K) Freely available
Right arrowOA All Versions of this Article:
35/suppl_1/D241    most recent
gkl850v2
gkl850v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Portugaly, E.
Right arrow Articles by Linial, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Portugaly, E.
Right arrow Articles by Linial, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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.

Database Issue

EVEREST: a collection of evolutionary conserved protein domains

Elon Portugaly*, Nathan Linial and Michal Linial1

School of Computer Science & Engineering 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 of 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 and Pfam A. 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
S. J. Sammut, R. D. Finn, and A. Bateman
Pfam 10 years on: 10 000 families and still growing
Brief Bioinform, May 1, 2008; 9(3): 210 - 219.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.