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Full-Text Articles in Life Sciences
Oligonucleotide Design For Whole Genome Tiling Arrays, Qin Dong
Oligonucleotide Design For Whole Genome Tiling Arrays, Qin Dong
Electronic Thesis and Dissertation Repository
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 …
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., Abu Sadat Md. Sayem
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., Abu Sadat Md. Sayem
Electronic Thesis and Dissertation Repository
Representing DNA sequences graphically and evaluating, as well as displaying, species’ relationships have been considered to be an important aspect of molecular biology research. A novel approach is proposed in this thesis that combines three methods: a) Chaos Game Representation (CGR), to portray quantitative characteristics of a DNA sequence as a black-and -white image, b) Structural Similarity (SSIM) index, an image comparison method, to compute pair-wise distances between these images, and c) Multidimensional Scaling (MDS), to visually display each sequence as a point in a two-dimensional Euclidean space. The proposed method produces a visual representation called Genome Distance Map (GDM) …