Overview

• Home: Introduction of qPrimerDB; What's New; Search content in the qPrimerDB;  Search primers for interested genes; Browse; Statistics of the qPrimerDB; Links to Browse, Tools, Downloads, Documents, Help and BioDB.
• Browse: Favorite organism; Plants; Animals; Others; Sorting by alphabets.
• Tools: qPrimerDB BLAST for conversion of gene ID; Design request and Result feedback form; 
• Downloads: Download best primers and all primers.
• Document: Manual; Pipeline; Statistics; Resource.
• Help: FAQ; Contact us.
• BioDB: Link to Biological Database platform (BioDB).

Homepage

                        

• Browse: users can browse interested organisms by choosing their classification and scientific name. Fox example, users could browse the primers of Arabidopsis thaliana by sequentially clicking "Plants", "Eudicotyledons" and "Arabidopsis thaliana" (corresponding to "1", "2" and "3" in the red rectangle) as the following figure. Primers of target organism then could be viewed. More detailed information can be accessed for each gene via the hyperlink in the blue rectangle in the primer ID ("4" in the red rectangle) and gene ID ("5" in the red rectangle) columns. For example, users can view the detailed information for best primer of AT1G72390 by clicking the hyperlink of primer ID A.thaliana.005900.v1, including gene description, primer pair description, hyperlink for ‘All primers for AT1G72390’, and amplicon and template sequences. The table of all primers for AT1G72390 could be viewed by clicking the hyperlinks ‘AT1G72390’ ("5" in the red rectangle) in ‘Best Primers for Arabidopsis thaliana’ page or ‘All primers for AT1G72390’ ("6" in the red rectangle) in ‘Details for primer A.thaliana.005900.v1’ page. Then, detailed information for each of all primers could be viewed by clicking the primer ID of interest ("7" in the red rectangle).

            

• Search and export primers for interested genes:  users can search primers by choosing the name(s) of the target organism(s) and inputting keywords (Gene or transcript ID: "ENST00000161863.8"; Primer ID: "H.sapiens.000100v1"; keywords: "YTH domain containing 2"). There are three steps from searching to result export. Taking ENST00000260810.9 and ENST00000161863.8 as an example, users should choose the organism name by sequentially clicking "Organisms" (1a) and "Homo sapiens" (1b) as the following figure in step 1. Then, the keywords for search query need to be entered in the search query box, such as "ENST00000260810.9 ENST00000161863.8" (2a). After clicking the "search" button (2b), the results will be returned immediately in step 2. For results export in step 3, users just need to click the check boxes (3a) before target genes, finally, click the button "Export to XLS" or "Export to JSON" (3b) to obtain searching results. Users could enter multiple keywords separated by space to retrieve primers of multiple target genes simultaneously.

          

Browse

• Browse by different group of organisms: browse by Favorites, Plants (Eudicotyledons, Monocotyledons, Other plants), Animals (Birds and Reptiles, Fish, Insecta, Mammalia, Other animals), Other eukaryotes (fungi) and Sorting by alphabets.
• Favorites: the following organisms were included (Animals: Apis mellifera, Bombyx mori, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Nasonia vitripennis; Plants: Arabidopsis thaliana, Glycine max, Oryza sativa, Physcomitrella patens, Solanum lycopersicum, Solanum tuberosum, Zea mays; Other eukaryotes: Saccharomyces cerevisiae)
• By alphabets: All the scientific names of 148 organisms were listed in alphabetical order.

Tools

• qPrimerDB BLAST: a set of tools built with NCBI-BLAST+, and used for searching homologous genes or converting gene IDs between different databases, retrieving gene-specific qPCR primers of target genes subsequently. It supports aligning aginst multiple databases. For example, if we would like to retrieve gene-specific qPCR primer for a gene with a different name in other databases, like "AtCDC5" gene in Arabidopsis thaliana. We could get the gene ID in the qPrimerDB using qPrimerDB BLAST as follows. In step 1, we need to choose the database by click "Database" (1a) and  "Arabidopsis thaliana" (1b), select the output format (table is necessary for getting qPCR primer) and hit number (1c), and enter the sequence in FASTA format or qPrimerDB identifiers each with a prefix "ID:" (1d). After clicking the submit button (1e), we could get the BLAST result in table format (1f). Finally, all the information (primer ID, gene ID, primer sequence, etc.) about query gene will be returned by clicking the subject name, which is marked in a blue rectangle.

       

• Design request: If the qPrimerDB doesn't cover the organism of your interest, users can send a feedback form to us and we will add the gene-specific qPCR primer pairs for you. But, please check the update news to confirm whether the primer design has already been planned for your interested organisms.
• Result feedback: users can submit the qPCR detection results to us (melting curve and/or gel electrophoresis), especially the specificity of primer pairs used, which will be included and displayed in the next version of qPrimerDB.

Downloads

• Primers: users can get the best primer and all primer of 148 organisms through choosing target organism (1-2) and clicking the download icon (3).