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dc.contributor.advisorCheng, Jianlin, 1972-eng
dc.contributor.authorAhmad, M. Mursaleen, 1985-eng
dc.date.issued2009eng
dc.date.submitted2009 Falleng
dc.descriptionTitle from PDF of title page (University of Missouri--Columbia, viewed on March 10, 2010).eng
dc.descriptionThe entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.eng
dc.descriptionThesis advisor: Dr. Jianlin Cheng.eng
dc.descriptionM.S. University of Missouri--Columbia 2009.eng
dc.description.abstract[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Polymerase chain reaction (PCR) amplification of specific regions of DNA has proven to be a powerful tool in molecular biology research. Synthetic short oligonucleotide DNA sequences (primers) provide specificity for the reaction by annealing to the target template DNA and providing the substrate for polymerase chain extension during the PCR. Primers are generally designed by extracting sequence matches from a single input DNA target with particular base composition, length, and position within the input DNA target. However, when the template DNA is from complex genomes or in mixtures of target DNAs, primer picking must be more sophisticated to enable discrimination of closely related sequences in the PCR. MUPrimer is a program to design allele-specific PCR primers that can discriminate among highly homologous gene sequences. The input target DNA includes of closely related sequences, making this software unique. User inputs include designating a master gene, primer positions, included and excluded regions, product length, primer T[subscript m], and maximum T[subscript m] difference allowed between forward and reverse primers. The software analyzes the sequences and returns primer pairs with a score that captures potential specificity of the primer based on the position of mismatches within a primer. The output is visual, displaying primer positions within the master sequence, a score for each primer, and an alignment of selected primer with the non-target sequences. MUPrimer is capable of providing PCR primers that enable allele-specific PCR amplification of specific target genes when in the presence of highly similar target sequences.eng
dc.description.bibrefIncludes bibliographical referenceseng
dc.format.extentvi, 56 pageseng
dc.identifier.oclc557591577eng
dc.identifier.urihttps://doi.org/10.32469/10355/6660eng
dc.identifier.urihttps://hdl.handle.net/10355/6660
dc.languageEnglisheng
dc.publisherUniversity of Missouri--Columbiaeng
dc.relation.ispartofcommunityUniversity of Missouri--Columbia. Graduate School. Theses and Dissertationseng
dc.rightsAccess is limited to the campuses of the University of Missouri.eng
dc.subject.lcshPolymerase chain reaction -- Computer programseng
dc.subject.lcshNucleotide sequence -- Computer programseng
dc.titleMUPrimer : a tool for finding allele specific PCR-primers for homologous gene sequenceseng
dc.typeThesiseng
thesis.degree.disciplineComputer science (MU)eng
thesis.degree.grantorUniversity of Missouri--Columbiaeng
thesis.degree.levelMasterseng
thesis.degree.nameM.S.eng


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