Skip Navigation

Bioinformatics 2005 21(7):932-937; doi:10.1093/bioinformatics/bti085
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) 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 (9)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Weiner, J.
Right arrow Articles by Bornberg-Bauer, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Weiner, J., 3rd
Right arrow Articles by Bornberg-Bauer, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Rapid motif-based prediction of circular permutations in multi-domain proteins

January Weiner, 3rd 1, Geraint Thomas 2 and Erich Bornberg-Bauer 1,*

1Division of Bioinformatics, School of Biology, Institute of Botany, The Westphalian Wilhelm's University of Münster Schlossplatz 4 D48149 Münster, Germany
2Faculty of Biological Sciences, The University of Leeds Leeds, UK

*To whom correspondence should be addressed.

Motivation: Rearrangements of protein domains and motifs such as swaps and circular permutations (CPs) can produce erroneous results in searching sequence databases when using traditional methods based on linear sequence alignments. Circular permutations are also of biological relevance because they can help to better understand both protein evolution and functionality.

Results: We have developed an algorithm, RASPODOM, which is based on the classical recursive alignment scheme. Sequences are represented as strings of domains taken from precompiled resources of domain (motif) databases such as ProDom. The algorithm works several orders of magnitude faster than a reimplementation of the existing CP detection algorithm working on strings of amino acids, produces virtually no false positives and allows the discrimination of true CPs from ‘intermediate’ CPs (iCPs). Several true CPs which have not been reported in literature so far could be identified from Swiss-Prot/TrEMBL within minutes.

Availability: Source codes, additional scripts, data and a web-based interface can be found on: http://www.uni-muenster.de/Biologie.Botanik/ebb/projects/raspodom/

Contact: ebb{at}uni-muenster.de


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
 Proc. Natl. Acad. Sci. USAHome page
L. Xie and P. E. Bourne
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
PNAS, April 8, 2008; 105(14): 5441 - 5446.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Beaussart, J. Weiner 3rd, and E. Bornberg-Bauer
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
Bioinformatics, July 15, 2007; 23(14): 1834 - 1836.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Viksna and D. Gilbert
Assessment of the probabilities for evolutionary structural changes in protein folds
Bioinformatics, April 1, 2007; 23(7): 832 - 841.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. Sanguinetti, N. D. Lawrence, and M. Rattray
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
Bioinformatics, November 15, 2006; 22(22): 2775 - 2781.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Pasek, J.-L. Risler, and P. Brezellec
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
Bioinformatics, June 15, 2006; 22(12): 1418 - 1423.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Weiner 3rd and E. Bornberg-Bauer
Evolution of Circular Permutations in Multidomain Proteins
Mol. Biol. Evol., April 1, 2006; 23(4): 734 - 743.
[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.