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Web-based primer design software for genome-scale genotyping by pyrosequencing.

Steven Ringquist·Christopher Pecoraro·Ying Lu·Alexis Styche·William A Rudert·Panayiotis V Benos·Massimo Trucco
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Abstract

Design of locus-specific primers for use during genetic analysis requires combining information from multiple sources and can be a time-consuming process when validating large numbers of assays. Data warehousing of genomic DNA sequences and genetic variations when coupled with software applications for optimizing the generation of locus-specific primers can increase the efficiency of assay development. Selection of oligonucleotide primers for PCR and Pyrosequencing (SOP3) software allows user-directed queries of warehoused data collected from the human and mouse genome sequencing projects. The software automates collection of DNA sequence flanking single-nucleotide polymorphisms (SNPs) as well as the incorporation of locus-associated functional information, such as whether the SNP occurs in an exon, intron, or untranslated region. SOP3 software accepts three types of user-directed input consisting of gene locus symbols, SNP reference sequence numbers, or chromosomal physical location. For human polymorphisms, SOP3 incorporates haplotype, ethnicity, and SNP validation attributes. The output is a list of oligonucleotide primers recommended for Pyrosequencing-based typing of genetic variations. SOP3 is available at the Division of Immunogenetics computational server found at http://imgen.ccbb.pitt.edu.

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AnimalsBase SequenceChromosomes, HumanDNA PrimersDiphosphatesGenomeGenomicsGenotypeHumansInternetMiceMolecular Sequence DataPolymerase Chain ReactionPolymorphism, Single NucleotideSequence Analysis, DNASoftwareUser-Computer InterfaceJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, Non-P.H.S.

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Steven Ringquist, Christopher Pecoraro, Ying Lu, Alexis Styche, William A Rudert, Panayiotis V Benos, Massimo Trucco. 2007. Web-based primer design software for genome-scale genotyping by pyrosequencing.. https://doi.org/10.1385/1-59745-377-3%3A25

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