MOTIVATION The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on Shannon entropy as a quality criterion. The practical motivation for our algorithm is oligonucleotide fingerprinting, a method for the simultaneous identification of sequences (cDNA or genomic DNA) ...

Short-oligonucleotide arrays typically contain multiple probes per gene. In genetical genomics applications a statistical model for the individual probe signals can help in separating "true" differential mRNA expression from "ghost" effects caused by polymorphisms, misdesigned probes, and batch effects. It can also help in detecting alternative splicing, start, or termination.

A new approach to respiratory syncytial virus subgroup differentiation has been developed on the basis of the hybridization of subgroup-specific synthetic oligonucleotides with viral mRNA. Two oligonucleotide probes were designed from the nucleotide sequences of an A and a B subgroup respiratory syncytial virus glycoprotein G gene. All 28 virus isolates tested were correctly classified by subgr...

UNLABELLED Oligonucleotide microarray probes are designed to match specific transcripts present in databases that are regularly updated. As a consequence probes should be checked every new database release. We thus developed an informatics tool allowing the semi-automatic update of probe collections of long oligonucleotides and applied it to the mouse RefSeq database. AVAILABILITY http://www....

Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-speci...