Skip Navigation


Bioinformatics Advance Access originally published online on January 21, 2009
Bioinformatics 2009 25(5):599-605; doi:10.1093/bioinformatics/btp047
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
25/5/599    most recent
btp047v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Sato, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sato, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Gclust: trans-kingdom classification of proteins using automatic individual threshold setting

Naoki Sato

Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan


  Abstract

Motivation: Trans-kingdom protein clustering remained difficult because of large sequence divergence between eukaryotes and prokaryotes and the presence of a transit sequence in organellar proteins. A large-scale protein clustering including such divergent organisms needs a heuristic to efficiently select similar proteins by setting a proper threshold for homologs of each protein. Here a method is described using two similarity measures and organism count.

Results: The Gclust software constructs minimal homolog groups using all-against-all BLASTP results by single-linkage clustering. Major points include (i) estimation of domain structure of proteins; (ii) exclusion of multi-domain proteins; (iii) explicit consideration of transit peptides; and (iv) heuristic estimation of a similarity threshold for homologs of each protein by entropy-optimized organism count method. The resultant clusters were evaluated in the light of power law. The software was used to construct protein clusters for up to 95 organisms.

Availability: Software and data are available at http://gclust.c.u-tokyo.ac.jp/Gclust_Download.html.

Contact: naokisat{at}bio.c.u-tokyo.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on December 16, 2008; revised on January 16, 2009; accepted on January 16, 2009

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
 Gen Biol EvolHome page
N. V. Sasaki and N. Sato
Elucidating Genome Structure Evolution by Analysis of Isoapostatic Gene Clusters using Statistics of Variance of Gene Distances
Gen Biol Evol, January 18, 2010; 2010(0): 1 - 12.
[Abstract] [Full Text] [PDF]

Home page
 DatabaseHome page
N. V. Sasaki and N. Sato
CyanoClust: comparative genome resources of cyanobacteria and plastids
Database, January 8, 2010; 2010(0): bap025 - bap025.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Nakao, S. Okamoto, M. Kohara, T. Fujishiro, T. Fujisawa, S. Sato, S. Tabata, T. Kaneko, and Y. Nakamura
CyanoBase: the cyanobacteria genome database update 2010
Nucleic Acids Res., January 1, 2010; 38(suppl_1): D379 - D381.
[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.