Electronic Thesis and Dissertation Repository

Thesis Format



Doctor of Philosophy


Computer Science


Ilie, Lucian


Oligonucleotides, or probes, are short, single-stranded fragments of DNA or RNA, designed to bind at a unique position in the target sequence. High specificity of oligonucleotides plays a crucial role in the accurate performance of several important applications such as PCR (polymerase chain reaction) amplification, microarrays, and FISH (fluorescence in situ hybridization) probes. The specificity of existing probes, including commercial ones from Agilent, is lower than expected, usually due to overreliance on the ability of BLAST to find similarities. When probe uniqueness is the goal, the shortcomings of BLAST are most clearly exposed, with bad consequences for the quality of the probes.

We propose two tools for designing probes for whole genome tiling and PCR primers, respectively. The new algorithms rely on the incomparably better ability of multiple spaced seeds to discover similarities, compared with BLAST. They produce more and better probes than existing state-of-the-art tools, the specificity of the new probes being nearly perfect.

Summary for Lay Audience

DNA carries genetic information and can also be manipulated to facilitate many health science research techniques. Oligonucleotides are short, single-stranded fragments of nucleic acids that can bind to a specific target that complementarily matches its own sequence. They are necessary for several molecular biology techniques such as DNA amplification and detection, in which oligonucleotide specificity directly influences their accuracy; for instance, the positive accuracy of nucleic acid testing in PCR assay, the widely used technique in the pandemic.

Oligonucleotides used to detect nucleic acids are called probes, while those used as starting points for enzymes to amplify nucleic acids are termed primers. Effectively designing unique probes and primers is a limiting step to succeed at these techniques. Currently, the publicly available programs of probe and primer designs are slow and unsatisfactory, which motivated us to optimize the performances. We propose two new algorithms that generate probes for whole genome tiling or PCR primers, with much higher specificity, and in a shorter amount of time, than the existing tools.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Available for download on Thursday, May 01, 2025