Date of Award

Spring 2004

Document Type

Thesis

Degree Name

Master of Science in Computational Biology - (M.S.)

Department

College of Computing Sciences

First Advisor

Gary Brewer

Second Advisor

Tamara M. Gund

Third Advisor

Michael Recce

Abstract

AUF 1, an A+U rich element (ARE) binding protein, plays an important role in mRNA decay. To identify the mRNAs that interact with AUF 1, mRNA derived from a human cardiac cDNA expression library was purified by AUF 1 affinity chromatography and cloned following RT-PCR. 261 sequences were obtained. The sequences were searched against two protein databases and four nucleic acid databases, and the sequence information and database search results were input into a local Microsoft Access database, BLAST-AUF 1, by Java applets for parsing document. Analysis of protein information by querying BLAST-AUF 1 identified 194 function-known proteins, which were classified into 14 categories. Another 20 clones represented uncharacterized genes encoding hypothetical proteins, which were submitted to a website for analysis of domain and function. The other 47 clones that failed to yield any protein information were located in some chromosomes by aligning their sequences with human genome sequence. The BLAST-AUF 1 database provides a data platform for further study of the expression profile of mRNAs that may be involved in AUF 1-dependent functional pathways.

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