Date of Award


Degree Type


Degree Name

Master of Science


Computer Science


Dr. Lucian Ilie

Second Advisor

Dr. Silvana Ilie


An oligonucleotide is a small piece of DNA or RNA molecule, which is designed to hybridize with a unique position in a target sequence. DNA oligonucleotides have many applications such as gene identification, PCR (polymerase chain reaction) amplification, or DNA microarrays. One of the crucial issues in designing good oligonucleotide is to minimize the chance of cross-hybridization. Various heuristic algorithms are used to filter out the unsuitable regions before checking for cross-hybridization. The most successful ones are based on seeds because of their efficiency and ability to tolerate mismatches. The quality of the seeds is essential in this process. We present a sound framework for evaluating seed quality for oligonucleotide design and show that multiple spaced seeds are expected to provide the best discrimination between oligos and non-oligos.



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