Thesis (Ph. D.)--Virginia Polytechnic Institute and State University, 1993. / Vita. Abstract. Includes bibliographical references (leaves 139-166). Also available via the Internet.

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1993. / Vita. Abstract. Includes bibliographical references (leaves 88-93). Also available via the Internet.

Thesis (M. Phil.)--University of Hong Kong, 2005. / Title proper from title frame. Also available in printed format.

Thesis (Ph. D.)--University of Texas at Austin, 2005. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--Washington State University, December 2006. / Includes bibliographical references.

No description available.

Motivation: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information. Results: Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples.

No description available.

A 30-mer oligonucleotide probe encoding the "A box" and anticodon loop regions of a human glycine tRNA gene was used to isolate a 581bp DNA fragment from a bovine genomic DNA library. Although the cross-hybridizing segment of DNA was found not to encode any tRNA gene or pseudogene, a region with homology to the "C-element" of the "BOV-tA" type Alulike artiodactyl retroposons was identified. This cross-hybridization was determined to be the result of conserved RNA polymerase III promoter elements in the probe portion of the tRNA gene and these repetitive elements. A microsatellite repeat (TC) was also found associated with this element. Future screening for bovine tRNA genes will require the use of a) longer probes and higher stringency hybridization conditions or b) the simultaneous screening with probes from the 5' and 3' ends of the gene which avoid the conserved Pol III promoter boxes.

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy