Selecting Degenerate Multiplex PCR Primers
Single Nucleotide Polymorphism (SNP) Genotyping is an important molecular genetics technique in the early stages of producing results that will be useful in the medical field. One of the proposed methods for performing SNP Genotyping requires amplifying regions of DNA surrounding a large number of SNP loci. In order to automate a portion of this method and make the use of SNP Genotyping more widespread, it is important to select a set of primers for the experiment. Selecting these primers can be formulated as the Multiple Degenerate Primer Design (MDPD) problem. An iterative beam-search algorithm, Multiple, Iterative Primer Selector (MIPS), is presented for MDPD. Theoretical and experimental analyses show that this algorithm performs well compared to the limits of degenerate primer design and the number of spurious amplifications should be small. Furthermore, MIPS outperforms an existing algorithm which was designed for a related degenerate primer selection problem. An implementation of the MIPS algorithm is available for research purposes from the website http://www.cse.wustl.edu/ zhang/software/mips.
Designing Of Degenerate Primers-Based Polymerase Chain Reaction (PCR) For Amplification Of WD40 Repeat-Containing Proteins Using Local Allignment Search Method
Degenerate primers-based polymerase chain reaction (PCR) are commonly used for isolation of unidentified gene sequences in related organisms. For designing the degenerate primers, we propose the use of local alignment search method for searching the conserved regions long enough to design an acceptable primer pair. To test this method, a WD40 repeat-containing domain protein from Beauveria bass...متن کامل
Amplification of multiple DNA sequences in a single Polymerase Chain Reaction (PCR) experiment, called Multiplex PCR (MPPCR), is a widely known laboratory technique that requires efficient selection of a set of synthetic strings called Degenerate Primers to result in successful PCR products. The Multiple Degenerate Primer Selection Problem (MDPSP) is a fundamental problem in molecular biology a...متن کامل
The multiplex polymerase chain reaction (MP-PCR) is a quick and an inexpensive technique in molecular biology for amplifying multiple DNA loci in a single Polymerase Chain Reaction (PCR). One of the criteria to achieve highly specific reaction products is to keep the concentration of the amplification primers low. In research, the dilemma associated with primer minimization for MP-PCR reactions...متن کامل
Genogroup I and II noroviruses detected in stool samples by real-time reverse transcription-PCR using highly degenerate universal primers.
Genogroup I noroviruses from five genetic clusters and genogroup II noroviruses from eight genetic clusters were detected in stool extracts using degenerate primers and single-tube, real-time reverse transcription-PCR (RT-PCR) with SYBR Green detection. Two degenerate primer sets, designated MON 431-433 and MON 432-434, were designed from consensus sequences from the major clusters of norovirus...متن کامل
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments...متن کامل