Method for design of an oliginucleotide array

Abstract

A method is provided allowing for automatic selection of enzymes to be used in protocols such as methylation profiling, chip-on-chip, and comparative genomic hybridization experiments. The method may also maximize the space on a micro array for a given experiment. This means that the results from the micro array are improved. The method also improves zero-in and focus of significant patterns on a micro array. This enhances the ability to distinguish two separate classes of samples, e.g. tumour vs. normal, aggressive vs. non-aggressive, male vs. female, etc. Furthermore, a computer readable medium and a device are also provided.

Description

field of invention [0001] The present invention relates generally to the field of oligonucleotide array validation. More particularly, the present invention relates to methods, and more particularly to computer readable media. Background of the invention [0002] An oligonucleotide array is a chip in which a large number of oligonucleotide sequences such as DNA sequences are immobilized in a specific pattern. [0003] Depending on which mechanism one wishes to study, different oligonucleotide arrays can be designed. For example, DNA methylation, which can be studied with a specific type of microarray called methylated oligonucleotide microarray analysis (MOMA), is the best-studied epigenetic mechanism of gene regulation. DNA methylation of so-called CpG-rich regions present in promoter regions is known to serve as a mechanism for gene silencing. CpG islands are portions of the genome rich in nucleotides C and G. [0004] Methods known to those skilled in the art for expe...

AI Technical Summary

Problems solved by technology

As many as possible are preferred, but even with high-density arrays, there is not enough space

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