Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1212K) Freely available
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (31)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sasson, O.
Right arrow Articles by Linial, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sasson, O.
Right arrow Articles by Linial, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 1 348-352
© 2003 Oxford University Press

ProtoNet: hierarchical classification of the protein space

Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial and Michal Linial*,1

School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel 1 Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel

*To whom correspondence should be addressed. Tel: +972 26585425; Fax: +972 26586448; Email: michall{at}mail.ls.huji.ac.il

ABSTRACT

The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. ProtoNet (version 1.3) is accessible in the form of an interactive web site at http://www.protonet.cs.huji.ac.il. ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes.


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
 BioinformaticsHome page
J. M. Joseph and D. Durand
Family classification without domain chaining
Bioinformatics, June 15, 2009; 25(12): i45 - i53.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. G. Tarcea, T. Weymouth, A. Ade, A. Bookvich, J. Gao, V. Mahavisno, Z. Wright, A. Chapman, M. Jayapandian, A. Ozgur, et al.
Michigan molecular interactions r2: from interacting proteins to pathways
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D642 - D646.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
M. Brilli, R. Fani, and P. Lio
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Brief Bioinform, January 1, 2008; 9(1): 34 - 45.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. Xiong, C. E. Bauer, and A. Pancholy
Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis
Microbiology, October 1, 2007; 153(10): 3548 - 3562.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Jayapandian, A. Chapman, V. G. Tarcea, C. Yu, A. Elkiss, A. Ianni, B. Liu, A. Nandi, C. Santos, P. Andrews, et al.
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D566 - D571.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
M.-J. Han and S. Y. Lee
The Escherichia coli Proteome: Past, Present, and Future Prospects
Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 362 - 439.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
R. L Marsden, J. A.G Ranea, A. Sillero, O. Redfern, C. Yeats, M. Maibaum, D. Lee, S. Addou, G. A Reeves, T. J Dallman, et al.
Exploiting protein structure data to explore the evolution of protein function and biological complexity
Phil Trans R Soc B, March 29, 2006; 361(1467): 425 - 440.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Uchiyama
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes
Nucleic Acids Res., January 25, 2006; 34(2): 647 - 658.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Rattei, R. Arnold, P. Tischler, D. Lindner, V. Stumpflen, and H. W. Mewes
SIMAP: the similarity matrix of proteins
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D252 - D256.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Bahir and M. Linial
ProTeus: identifying signatures in protein termini
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W277 - W280.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. Kifer, O. Sasson, and M. Linial
Predicting fold novelty based on ProtoNet hierarchical classification
Bioinformatics, April 1, 2005; 21(7): 1020 - 1027.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Q. J. Su, L. Lu, S. Saxonov, and D. L. Brutlag
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D178 - D182.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kaplan, O. Sasson, U. Inbar, M. Friedlich, M. Fromer, H. Fleischer, E. Portugaly, N. Linial, and M. Linial
ProtoNet 4.0: A hierarchical classification of one million protein sequences
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D216 - D218.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Mohseni-Zadeh, A. Louis, P. Brezellec, and J.-L. Risler
PHYTOPROT: a database of clusters of plant proteins
Nucleic Acids Res., January 1, 2004; 32(90001): D351 - 353.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kaplan, A. Vaaknin, and M. Linial
PANDORA: keyword-based analysis of protein sets by integration of annotation sources
Nucleic Acids Res., October 1, 2003; 31(19): 5617 - 5626.
[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.