BioInformatics, Phylogenetics, and Aspartate Transcarbamoylase

In this research, the necessity of understanding and using bioinformatics is demonstrated using the enzyme aspartate transcarbamoylase (ATCase) as the model enzyme. The first portion of this research focuses on the use of bioinformatics. A partial sequence of the pyrB gene found in Enterococcus faecalis was submitted to GenBank and was analyzed against the contiguous sequence from its own genome project. A BLAST (Basic Local Alignment Search Tool; Atschul, et al., 1990) was performed in order to hypothesize the remaining portion of the gene from the contiguous sequence. This allowed a global comparison to other known aspartate transcarbamoylases (ATCases) and once deduced, a translation of the sequence gave the stop codon and thus the complete sequence of the open reading frame. When this was complete, upstream and downstream primers were designed in order to amplify the gene from genomic DNA. The amplified product was then sequenced and used later in phylogenetic analyses concerning the evolution of ATCase. The second portion of this research involves taking multiple ATCase nucleotide sequences and performing phenetic and phylogenetic analyses of the archaea and eubacter families. From these analyses, ancestral relationships which dictate both structure and function were extrapolated from the data and discussed.

Grantor dc:publisher

University of North Texas

Year dc:date

2000

Author dc:creator

• Cooke, Patrick Alan

Contributors dc:contributor

• O'Donovan, Gerard A.
• Shanley, Mark S.
• White, Olivia
• Theriot, Leroy James
• Planz, John

• Bioinformatics.
• Phylogeny.
• Pyrimidine nucleotides -- Metabolism.
• genome project
• genetics
• phylogenetic analyses
• bioinformatics

Statement dc:rights

• Use restricted to UNT Community
• Copyright
• Cooke, Patrick Alan
• Copyright is held by the author, unless otherwise noted. All rights reserved.

Language dc:language

English

Identifier

oclc: 49937862
untcat: b2374893
https://digital.library.unt.edu/ark:/67531/metadc2580/
ark: ark:/67531/metadc2580

OAI identifier oai:identifier

info:ark/67531/metadc2580