Genes homologous to a set of known, aligned, genes can be found by screening DNA libraries with PCR. PCR primers for such screens are commonly designed via a method described by Sells and Chernoff (1995). This standard design method does not make use of information about the evolutionary relationship between the known genes. The present study investigated the efficacy of using information about evolutionary relationships (inferred from the sequence data) in the design of PCR primers. This study compares the standard primer design method (represented herein by a modified multinomial distribution) with evolutionary model based primer design methods. The primer design method that, given an alignment of known sequences with one sequence left out, assigned a higher probability, on average, to the left-out sequence, was defined as the better method. By this measure of relative performance, an evolutionary model based primer design method sensitive to states correlated across sites of a sequence, outperformed the standard method, on the alignments studied.
| Identifer | oai:union.ndltd.org:NCSU/oai:NCSU:etd-10232003-122816 |
| Date | 24 November 2003 |
| Creators | Thompson, Denis |
| Contributors | Henry Schaffer, Jeff Thorne, Charlie Eugene Smith, Michael Purugganan |
| Publisher | NCSU |
| Source Sets | North Carolina State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://www.lib.ncsu.edu/theses/available/etd-10232003-122816/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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