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Primer Design (primer + design)
Selected AbstractsReal-time primer design for DNA chipsCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 9 2004H. Simmler Abstract The design of PCR or DNA chip experiments is a time-consuming process where bioinformatics is extensively used. The selection of the primers, which are immobilized on the DNA chip, requires a complex algorithm. Based on several parameters an optimized set of primers is automatically determined for a given gene sequence. This paper describes a parallel architecture which performs the optimization of the primer selection on a hardware accelerator. In contrast to the pure software approach, the parallel architecture gains a speedup of factor 500 using a PCI-based hardware accelerator. This approach allows an optimization of a specified primer set in real time. Copyright © 2004 John Wiley & Sons, Ltd. [source] Advances in molecular ecology: tracking trophic links through predator,prey food-websFUNCTIONAL ECOLOGY, Issue 5 2005S. K. SHEPPARD Summary 1It is not always possible to track trophic interactions between predators and prey by direct observation. This is especially true when observing small or elusive animals with cryptic food-web ecology. Gut and/or faecal analysis can sometimes allow prey remains to be identified visually but is only possible when a component of the diet is resistant to digestion. In some cases there are no solid remains, and when there are it can lead to bias in interpretation of prey choice. 2Numerous invasive and non-invasive methods have been developed to characterize predator,prey interactions but two principal areas dominate ,molecular' research. These are reviewed under the headings of monoclonal antibodies and DNA-based techniques. 3Early ,molecular' studies of predator,prey food webs were dominated by the development of monoclonal antibodies. These methods continue to be used for mass-screening of field-collected arthropods for insect-specific proteins. 4The application of species-specific primer design, polymerase chain reaction (PCR), restriction fragment length polymorphism analysis (RFLP), DNA cloning and sequencing, comparative sequence analysis (e.g. BLAST; basic local alignment search tool), high-resolution gel electrophoresis, Temperature/denaturing gradient gel electrophoresis (TGGE/DGGE) and automated fragment analysis with fluorescent probes is reviewed. The development of molecular techniques for use in predator,prey studies is primarily limited by their cost and the development of new procedures and equipment that complement them. [source] INVITED REVIEW: Molecular analysis of predation: a review of best practice for DNA-based approachesMOLECULAR ECOLOGY, Issue 4 2008R. A. KING Abstract Molecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessible to those new to this field or from a different molecular biology background. Optimization begins with field collection, sample preservation, predator dissection and DNA extraction techniques, all designed to ensure good quality, uncontaminated DNA from semidigested samples. The advantages of nuclear vs. mitochondrial DNA as primer targets are reviewed, along with choice of genes and advice on primer design to maximize specificity and detection periods following ingestion of the prey by the predators. Primer and assay optimization are discussed, including cross-amplification tests and calibratory feeding experiments. Once primers have been made, the screening of field samples must guard against (through appropriate controls) cross contamination. Multiplex polymerase chain reactions provide a means of screening for many different species simultaneously. We discuss visualization of amplicons on gels, with and without incorporation of fluorescent primers. In more specialized areas, we examine the utility of temperature and denaturing gradient gel electrophoresis to examine responses of predators to prey diversity, and review the potential of quantitative polymerase chain reaction systems to quantify predation. Alternative routes by which prey DNA might get into the guts of a predator (scavenging, secondary predation) are highlighted. We look ahead to new technologies, including microarrays and pyrosequencing, which might one day be applied to this field. [source] Isolation of sixteen autosomal loci and a sex-linked polymorphic microsatellite locus from the Milne-Edwards' sportive lemur (Lepilemur edwardsi)MOLECULAR ECOLOGY RESOURCES, Issue 1 2009M. CRAUL Abstract We isolated 21 microsatellites from the Milne-Edwards' sportive lemur, Lepilemur edwardsi. Eighteen microsatellite sequences possessed sufficient flanking DNA for primer design. Seventeen loci amplified and were found to be polymorphic displaying two to 17 alleles in 32 unrelated individuals from a population from the National Park of Ankarafantsika in northwest Madagascar. One locus (Led-12) was found to be sex linked located on the X chromosome and can be used to sex-type 40% of female L. edwardsi lemurs. These 17 loci were characterized to investigate family structure and the phylogeography of L. edwardsi. [source] msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer designMOLECULAR ECOLOGY RESOURCES, Issue 1 2008BRANT C. FAIRCLOTH Abstract msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta -formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/. [source] Characterization of 12 microsatellite markers in Serranus cabrilla (Pisces: Serranidae)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006J. CARRERAS-CARBONELL Abstract The commercial comber Serranus cabrilla is widely distributed in the Atlanto-Mediterranean region, inhabiting a great variety of habitats and depths. We developed primers for 12 polymorphic microsatellite loci to analyse the genetic structure between comber populations and between their colour morphs in order to establish correct fisheries management. Characterization of 25 individuals from Columbretes Islands (Spain) showed an average large number of alleles (9.5 ± 1.3) and observed heterozygosity (0.657 ± 0.06). Only two loci showed significant departure from Hardy,Weinberg equilibrium. We found no evidence of linkage disequilibrium between pairs of loci. We rejected for primer design one clone with a microsatellite within the transposable element TX_FR2. [source] DOGSET: pre-designed primer sets for fine-scale mapping and DNA sequence interrogation in the dogANIMAL GENETICS, Issue 4 2009A. K. Wong Summary DOGSET is an online resource that provides access to primer sequences that have been computationally mined from the reference genome using heuristic algorithms. The electronic repository includes PCR primers corresponding to 32 135 markers for genetic mapping and 334 657 sequence-tagged gene elements for targeted re-sequencing and mutation discovery. A customized report that tailors primer design to wet bench protocols can be exported for a region of interest by specifying genome coordinates in a graphical user interface. [source] Single nucleotide polymorphism (SNP) discovery in porcine expressed genesANIMAL GENETICS, Issue 3 2002S. C. Fahrenkrug High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs. [source] Specific PCR product primer design using memetic algorithmBIOTECHNOLOGY PROGRESS, Issue 3 2009Cheng-Hong Yang Abstract To provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product size. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this article, a memetic algorithm (MA) is proposed to solve primer design problems associated with providing a specific product size for PCR experiments. The MA is compared with a genetic algorithm (GA) using an accuracy formula to estimate the quality of the primer design and test the running time. Overall, 50 accession nucleotide sequences were sampled for the comparison of the accuracy of the GA and MA for primer design. Five hundred runs of the GA and MA primer design were performed with PCR product lengths of 150,300 bps and 500,800 bps, and two different methods of calculating Tm for each accession nucleotide sequence were tested. A comparison of the accuracy results for the GA and MA primer design showed that the MA primer design yielded better results than the GA primer design. The results further indicate that the proposed method finds optimal or near-optimal primer sets and effective PCR products in a dry dock experiment. Related materials are available online at http://bio.kuas.edu.tw/ma-pd/. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] | ||||||||||