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Primer databases | Quantitative PCR data analysis

Primer databases for PCR data analysis.

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A manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.
Provides an interactive and information-rich web graphical interface to display search and BLAST results as table-based descriptions and associated links. The qPrimerDB is a comprehensive primer database with a web frontend that provides pre-computed gene-specific quantitative polymerase chain reaction (qPCR) primer pairs. It also enables batch download of best gene-specific qPCR primer pairs. This online resource constitutes a valuable resource for gene expression analysis and will save precious time for researchers.
A database of virus-specific oligonucleotides. The VirOligo database collects virus-specific oligonucleotides for virus detection from published literature. The database consists of two tables, Common data and Oligo data. The Oligo data table contains PCR primers and hybridization probes used for detection of viral nucleic acids and the Common data table contains the experimental conditions used in their detection. Each oligonucleotide entry contains links to PubMed, GenBank, NCBI Taxonomy databases and BLAST.
A database to help viruses detection. MRPrimerV database contains 152,380,247 PCR primer pairs for detection of 1,818 viruses, covering 7,144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22,192 variants of 532 RefSeq RNA viruses. The public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.
Wheat D Genome Specific Marker Resource
A database of genetic and physical maps, genetic markers and marker sequences for wheat D Genome, accumulates and releases up-to-date information on Ae.tauschii genome sequencing. Wheat D Genome Specific Marker Resource allows users to search for marker/probe sequences within specific deletion bins or individual chromosomes by a simple BLAST analysis or marker ID input. PCR primers designed to amplify the marker regions are provided and available for download, providing an easy and effective marker system for mapping of individual genes/traits of interest.
HIVoligoDB / The HIV oligonucleotide database
Provides a set of oligonucleotides and genomic regions that can be used to improve the efficiency of Human Immunodeficiency Virus (HIV) epidemiological studies and nucleic acid-based assays. HIVoligoDB is a free resource with detailed records of oligonucleotides to study HIV-1 and HIV-2. The database contains more than 300 HIV-1 (primers and 144 probes) and more than 60 HIV-2 oligonucleotides (primers and probes) retrieved from peer-reviewed publications and the NCBI Probe Database.
OcaPPI-Db / Oligonucleotide Capture Probes for Pathogen Identification Database
Provides an oligonucleotide hybridization capture probe database targeting virulence factors and genes used to discriminate the National Institute of Allergy and Infectious Diseases (NIAID)’s bacterial pathogens priority list. OcaPPI-Db contains a set of 1,685 oligonucleotide probes allowing for the detection and identification of 245 biomarkers specific for 30 bacterial biothreat agents up to the species level. This probe set can be used in its entirety to provide a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to user’s needs.
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