ROSO: optimizing oligonucleotide probes for microarrays

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چکیده

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ROSO: optimizing oligonucleotide probes for microarrays

UNLABELLED ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set. AVAILABILITY The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. SUPPLEMENT...

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Fabrication of DNA microarrays using unmodified oligonucleotide probes.

Microarrays printed on glass slides are often constructed by covalently linking oligonucleotide probes to a derivatized surface. These procedures typically require relatively expensive amine- or thiol-modified oligonucleotide probes that add considerable expense to larger arrays. We describe a system by which unmodified oligonucleotide probes are bound to either nonderivatized or epoxy-silane-d...

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Specific and nonspecific hybridization of oligonucleotide probes on microarrays.

Gene expression analysis by means of microarrays is based on the sequence-specific binding of RNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving sequences other than the intended target is problematic because it adds a chemical background to the signal, which is not related to the expression degree of the target gene. The artic...

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Oligo Design: a computer program for development of probes for oligonucleotide microarrays.

Oligonucleotide microarrays have demonstrated potential for the analysis of gene expression, genotyping, and mutational analysis. Our work focuses primarily on the detection and identification of bacteria based on known short sequences of DNA. Oligo Design, the software described here, automates several design aspects that enable the improved selection of oligonucleotides for use with microarra...

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An Efficient Covalent Coating on Glass Slides for Preparation of Optical Oligonucleotide Microarrays

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2004

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btg401