论文COMPUTATIONAL METHODS FOR RATIONAL OLIGONUCLEOTIDE PCR PRIMER DESIGN AND ANALYSIS TWO SCENARIOS USI.docVIP

Computational Methods for Rational Oligonucleotide PCR Primer Design and Analysis: Two Scenarios Using GCG￥’s SeqLab. ‘Not your ordinary primer design.’ The two scenarios: 1) A complicated case where the target DNA is unknown and the sequences are ‘difficult’ to align — the “guessmer” — useful for discovering genes in organisms where they have not yet been identified when the gene’s encoded protein sequence is known in several other, related organisms. Here the example is the prion gene in primates; and 2) A case that you can do on your own where all the DNA sequences are known and ‘easily’ aligned — the Human Papilloma Virus major capsid protein L1 — type and strain differentiation. Fall 2006; a GCG￥ Wisconsin Package? SeqLab? tutorial for Florida State University sponsored by the School of Computational Science6 (SCS). Author and Instructor: Steven M. Thompson Steve Thompson BioInfo 4U 2538 Winnwood Circle Valdosta, GA, USA 31601-7953 stevet@ 229-249-9751 ￥GCG is the Genetics Computer Group, part of Accelrys Inc., producer of the Wisconsin Package( for sequence analysis. ( 2006 BioInfo 4U Steven M. Thompson Introduction The Polymerase Chain Reaction, PCR, developed at Cetus Corporation by Kary Mullis in the mid ‘80’s (Saiki, et al., 1988), for which he won the Nobel Prize, and patented by Hoffman La Roche and Perkins-Elmer Corporation, has revolutionized modern molecular biology. From Jurassic Park scenarios in popular novels, to everyday research in countless laboratories across the world, to cutting-edge forensic pathology techniques, PCR is being used to analyze tinier concentrations of DNA than ever before imagined possible. PCR allows the investigator to analyze any stretch of DNA in any organism where at least some sequence information is known, either in that organism or in related organisms. It can isolate, and amplify up to around a million-fold, just a few molecules of DNA from complex environmental mixtures, even where the DNA is significantly d