Skip Navigation

Nucleic Acids Research 2006 34(Web Server issue):W356-W361; doi:10.1093/nar/gkl309
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1757K) Freely available
Right arrow Screen PDF (393K) Freely available
Right arrow A corrigendum has been published
Right arrow A corrigendum has been published
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 Hsu, C.-M.
Right arrow Articles by Liu, B.-J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hsu, C.-M.
Right arrow Articles by Liu, B.-J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences

Chen-Ming Hsu, Chien-Yu Chen1,* and Baw-Jhiune Liu

Department of Computer Science and Engineering, Yuan Ze University Chung-Li, 320, Taiwan, Republic Of China 1 Department of Bio-Industrial Mechatronics Engineering, National Taiwan University Taipei, 106, Taiwan, Republic Of China

*To whom correspondence should be addressed. Tel: +886 2 33665334; Fax: +886 2 23627620; Email: cychen{at}mars.csie.ntu.edu.tw

Received February 14, 2006. Revised March 2, 2006. Accepted April 11, 2006.

This paper presents a web service named MAGIIC-PRO, which aims to discover functional signatures of a query protein by sequential pattern mining. Automatic discovery of patterns from unaligned biological sequences is an important problem in molecular biology. MAGIIC-PRO is different from several previously established methods performing similar tasks in two major ways. The first remarkable feature of MAGIIC-PRO is its efficiency in delivering long patterns. With incorporating a new type of gap constraints and some of the state-of-the-art data mining techniques, MAGIIC-PRO usually identifies satisfied patterns within an acceptable response time. The efficiency of MAGIIC-PRO enables the users to quickly discover functional signatures of which the residues are not from only one region of the protein sequences or are only conserved in few members of a protein family. The second remarkable feature of MAGIIC-PRO is its effort in refining the mining results. Considering large flexible gaps improves the completeness of the derived functional signatures. The users can be directly guided to the patterns with as many blocks as that are conserved simultaneously. In this paper, we show by experiments that MAGIIC-PRO is efficient and effective in identifying ligand-binding sites and hot regions in protein–protein interactions directly from sequences. The web service is available at http://biominer.bime.ntu.edu.tw/magiicpro and a mirror site at http://biominer.cse.yzu.edu.tw/magiicpro.


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
 Nucleic Acids ResHome page
D. T.-H. Chang, T.-Y. Chien, and C.-Y. Chen
seeMotif: exploring and visualizing sequence motifs in 3D structures
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W552 - W558.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T.-Y. Chien, D. T.-H. Chang, C.-Y. Chen, Y.-Z. Weng, and C.-M. Hsu
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W291 - W296.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C.-T. Su, C.-Y. Chen, and C.-M. Hsu
iPDA: integrated protein disorder analyzer
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W465 - W472.
[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.