PhylArray: phylogenetic probe design algorithm for microarray.
BACKGROUND
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.
Militon
Cécile
C
Génomique Intégrée des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des Cézeaux, France.
Rimour
Sébastien
S
Missaoui
Mohieddine
M
Biderre
Corinne
C
Barra
Vincent
V
Hill
David
D
Moné
Anne
A
Gagne
Geneviève
G
Meier
Harald
H
Peyretaillade
Eric
E
Peyret
Pierre
P
D000465:Algorithms; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D018390:Gene Targeting / Q000379:methods*; D017403:In Situ Hybridization / Q000379:methods*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes