Provides polymerase chain reaction (PCR) and quantitative PCR (qPCR) primers. PrimerBank is a public database for the retrieval of PCR and qPCR primers containing about 400 000 primers that cover 36 928 human and mouse genes, corresponding to around 94% of all known protein-coding gene sequences. Users can access all stored information (primer sequences and annotations, primer validation data, as well as gene annotations) from the search interface.
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.
Delivers primer and probe information. RTPrimerDB integrates primer sequences, target gene and organism information, mapping data, in silico evaluation characteristics, user feedback, links to citations, assays for the same target and external databases. It aims to solve the problem of laborious primer design and assay evaluation for quantification or detection of the same nucleic acid target sequences by different individuals.
Enables to retrieve gene or transcript-specific primers for several species genes in assembled chromosomes annotated in the Ensembl database. GETPrime is a primer database supported by a platform that combines and automates several features critical for optimal quantitative real-time polymerase chain reaction (qPCR) primer design. This database provides gene-specific read-out in easy-to-retrieve and graphical fashion.
A registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, SNP discovery, gene expression, gene silencing and gene mapping. Probe also includes information on reagent distributors, probe effectiveness and computed sequence similarities.
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.
Provides oligonucleotide capture sequences that span the human genome. OligoGenome offers functions to browse, filter and download capture oligonucleotide sequences based upon user queried genomic regions and annotation-based constraints. It allows users to build query both inside and outside of the coding regions of human genome. The database can be used as a useful resource for other selective circularization technologies.
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.
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.
Deals with small non-coding RNAs (ncRNAs). sRNAPrimerDB is composed of multiple primer designing programs, combined with calculated primers. It allows users to search and design primers for small ncRNAs, such as miRNAs and piRNAs. The database is composed of eight divisions including a section for designing, a bank of pre-designed primers and probes, a searching tool as well as links towards scientific literature and resources.
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.
Represents a genome-wide homogeneous and specific primer-pair database in Arabidopsis. AtRTPrimer provides a reliable primer pair of a target gene for singleplex polymerase chain reaction (PCR) experiments except genes having unknown alternative splicing forms. Researchers can properly select pre-designed primer pairs of a target gene for their desired types of RTPCR by changing the filtering condition.
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.
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.
Provides a repository for verified chromatin immunoprecipitation (ChIP) quantitative polymerase chain reaction (qPCR) oligonucleotide sequences. ChIPprimersDB collects published ChIP primer sequences. It includes data on the antibodies used and species, cell line or tissue associated. This database collects more than 1000 primers with more than 1100 entries and 400 genes categorized in 14 species.
Provides optimized primers for human and mouse RefSeq genes. qPrimerDepot contains primers sets designed to be used under uniform annealing temperatures. This database is a valuable resource for real-time reverse transcription (qRT) applications, especially in circumstances requiring high throughput detection of rare transcripts in curated and/or patient-derived samples that often contain unavoidable contamination with genomic DNA.
Serves as a specific oligo repository of probe, siRNA and primer design for human genome. SpecificDB is based on an integration of ANN and BLAST (IAB) algorithm to predict and identify specific N-mer oligos through polymerase chain reaction experiments. The web platform also offers several tools for microarray analysis and genome-wide iterative enrichment analysis.
1 - 7 of 7
0 - 0 of 0