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  • Genomic Resources for Zebrafish

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MGH site offers this tool which searches for a supercontig, scaffold, or finished BAC clone by name or accession number, derives all di- and tri- nucleotide repeat sequences in the supercontig, masks the sequence around the repeats for larger zebrafish repetitive sequences and then designs unique sequence primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects. This site also offers a tool to search for marker primer pairs by chromosome coordinates (3MB chromosome segments max.)

The qPrimerDB database (real-time quantitative PCR Primer Database), https://biodb.swu.edu.cn/qprimerdb) is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 516 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice, and maize. The qPrimerDB provides an interactive and information-rich web graphical interface to display search and BLAST results as table-based descriptions and associated links. In this database, we provide 9,273,735 of the best primer pairs for each gene based on primer pair coverage (PPC), as well as 68,653,054 alternative gene-specific primer pairs, which can be conveniently batch downloaded. We validated the specificity and efficiency of the qPCR primer pairs for 66 randomly selected genes in six different organisms through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be updated routinely.

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