Web-based primer design software for genome-scale genotyping by pyrosequencing.
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.
Ringquist
Steven
S
Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Pecoraro
Christopher
C
Lu
Ying
Y
Styche
Alexis
A
Rudert
William A
WA
Benos
Panayiotis V
PV
Trucco
Massimo
M
D000818:Animals; D001483:Base Sequence; D002877:Chromosomes, Human / Q000235:genetics; D017931:DNA Primers / Q000235:genetics*; D011756:Diphosphates / Q000378:metabolism*; D016678:Genome; D023281:Genomics; D005838:Genotype; D006801:Humans; D020407:Internet; D051379:Mice; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers; D011756:Diphosphates