Award Date


Degree Type


Degree Name

Master of Science (MS)


Biological Science

First Committee Member

Marcella McClure

Number of Pages



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.


Ancestry; Approach; Bioinformatic; Common; Dependent; Polymerases; Rna

Controlled Subject

Molecular biology

File Format


File Size

2129.92 KB

Degree Grantor

University of Nevada, Las Vegas




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