Skip Navigation


Bioinformatics Advance Access originally published online on August 12, 2007
Bioinformatics 2007 23(19):2550-2557; doi:10.1093/bioinformatics/btm392
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
23/19/2550    most recent
btm392v1
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 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 (1)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Militon, C.
Right arrow Articles by Peyret, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Militon, C.
Right arrow Articles by Peyret, P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PhylArray: phylogenetic probe design algorithm for microarray

Cécile Militon 1,{dagger}, Sébastien Rimour 1,2,{dagger}, Mohieddine Missaoui 1,2, Corinne Biderre 1, Vincent Barra 2, David Hill 2, Anne Moné 1, Geneviève Gagne 1, Harald Meier 3, Eric Peyretaillade 1 and Pierre Peyret 1,*

1Génomique Intégrée des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des Cézeaux, 2LIMOS UMR CNRS 6158, Blaise Pascal University, Clermont-Ferrand II, BP 10125, 63177 Aubière Cedex, France and 3Lehrstuhl für Rechnertechnik und Rechnerorganisation, Institut für Informatik, Technische Universität München, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial ‘black-box’, the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality.

Results: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called ‘PhylArray’, designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.

Availability: http://fc.isima.fr/~rimour/phylarray/

Contact: pierre.peyret{at}univ-bpclermont.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Thomas Lengauer

Received on April 3, 2007; revised on July 18, 2007; accepted on July 27, 2007

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
H. Rehrauer, S. Schonmann, L. Eberl, and R. Schlapbach
PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays
Bioinformatics, August 15, 2008; 24(16): i83 - i89.
[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.