Do RNA-dependent polymerases share common ancestry? A bioinformatic approach

Bioinformatics is the use of computational methods to perform hypothesis-driven research that generates new knowledge from existing biological databases. For any bioinformatic analysis, it is important that the most accurate method(s) be used. The first portion of this thesis is a comparative evaluation of six programs designed for the local alignment of protein sequences. The results demonstrate that two of the programs, MEME and PROBE, outperform all other programs (BLOCKMAKER, ITERALIGN, MATCHBOX, and PIMA). The second portion of this thesis uses MEME and PROBE in an attempt to locate an ordered-series-of-motifs (OSM) among two groups of RNA-dependent polymerases, the large (L) protein from viruses in the order Mononegavirales and the reverse transcriptase (RT) protein from retroviruses and retroid agents. An OSM was not detected among the L and RT proteins, suggesting that they are not homologs. This result also supports the hypothesis that all RNA-dependent polymerases do not share common ancestry.

Name thesis:degree_name

Master of Science (MS)

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Biological Science

Grantor dc:publisher

University of Nevada, Las Vegas

Year

1999

Author dc:creator

• Hudak, Julianna

Contributors dc:contributor

• Marcella McClure

Statement dc:rights

• IN COPYRIGHT. For more information about this rights statement, please visit http://rightsstatements.org/vocab/InC/1.0/

Language dc:language

English

Identifier

https://oasis.library.unlv.edu/rtds/1079

OAI identifier oai:identifier

oai:oasis.library.unlv.edu:rtds-2078