Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (523K) 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
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Thompson, J. D.
Right arrow Articles by Poch, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Thompson, J. D.
Right arrow Articles by Poch, O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 24 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 4 1298-1307
© 2004 Oxford University Press

LEON: multiple aLignment Evaluation Of Neighbours

Julie D. Thompson, Véronique Prigent and Olivier Poch*

Laboratoire de Biologie et Genomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France

*To whom correspondence should be addressed. Tel: +33 3 88 65 32 00; Fax: +33 3 88 65 32 01; Email: poch{at}igbmc.u-strasbg.fr

Sequence alignments are fundamental to a wide range of applications, including database searching, functional residue identification and structure prediction techniques. These applications predict or propagate structural/functional/evolutionary information based on a presumed homology between the aligned sequences. If the initial hypothesis of homology is wrong, no subsequent application, however sophisticated, can be expected to yield accurate results. Here we present a novel method, LEON, to predict homology between proteins based on a multiple alignment of complete sequences (MACS). In MACS, weak signals from distantly related proteins can be considered in the overall context of the family. Intermediate sequences and the combination of individual weak matches are used to increase the significance of low-scoring regions. Residue composition is also taken into account by incorporation of several existing methods for the detection of compositionally biased sequence segments. The accuracy and reliability of the predictions is demonstrated in large-scale comparisons with structural and sequence family databases, where the specificity was shown to be >99% and the sensitivity was estimated to be ~76%. LEON can thus be used to reliably identify the complex relationships between large multidomain proteins and should be useful for automatic high-throughput genome annotations, 2D/3D structure predictions, protein–protein interaction predictions etc.


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
M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Perin
GreenPhylDB: a database for plant comparative genomics
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D991 - D998.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Biol. CellHome page
J. Muller, Y. Oma, L. Vallar, E. Friederich, O. Poch, and B. Winsor
Sequence and Comparative Genomic Analysis of Actin-related Proteins
Mol. Biol. Cell, December 1, 2005; 16(12): 5736 - 5748.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
V. Prigent, J. C. Thierry, O. Poch, and F. Plewniak
DbW: automatic update of a functional family-specific multiple alignment
Bioinformatics, April 15, 2005; 21(8): 1437 - 1442.
[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.