Oligonucleotide Design for Whole Genome Tiling Arrays

Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow oligonucleotides that are too similar with non-targets, thus enabling unwanted cross-hybridization. We present a new program, BOND-tile, that produces much better tiling arrays, as shown by extensive comparison with leading programs.

Name thesis:degree_name

M Sc

Discipline thesis:degree_discipline

Computer Science

Grantor dc:publisher

The University of Western Ontario

Year dc:date.issued

2014

Author dc:creator

• Dong, Qin

Advisor dc:contributor.advisor

• Lucian Ilie

• DNA
• oligonucleotide
• tiling arrays
• microarrays

Language dc:language.iso

en_ca

Handle dc:identifier.uri

https://hdl.handle.net/20.500.14721/36910

OAI identifier oai:identifier

oai:uwo.scholaris.ca:20.500.14721/36910