Next-Gen Sequence Databases & sRNA Tools
Produced by the Meyers Lab at the UC Davis Genome Center
About Us
Our research group focuses on many aspects of plant small RNAs. This includes their primary role in regulation of genes and transposable elements, but also their biogenesis and evolution. For nearly a decade, we’ve been fascinated by their roles in plant reproduction. To advance these research aims, we have developed technologies including small RNA sequencing, sequencing of cleaved target RNAs, a wide variety of informatics tools (found on this site), and together with key collaborating experts in microscopy, imaging techniques to localize and quantify RNAs.
We are actively applying these methods to a variety of questions about small RNA biology and gene expression, particularly in crop plants, but also several models. See our research and publications.
Our Databases
We have developed a series of online databases which come with customized web interfaces to handle and display “next-gen” sequencing data of different types for a number of organisms and closely related varieties. Our websites are built on a common set of interfaces and are equipped with various graphical and analytical tools that allow the user to retrieve and analyze the data.
These data are freely available, but we ask that you cite this web page or related publications; most libraries have been published as part of specific papers, but the best general citation for the website is Nakano et al. (2019) Plant Physiology. We would also like to know that you have found our data to be useful, so please let us know if you use data from this page.
Organisms
Databases
Libraries
Click the “+” sign to show database links for each organism.
Note: Those links marked with “*” are excluded from the database and library totals above.
Malus domestica
Arabidopsis thaliana
sRNA, sRNA2, sRNA3, sRNA_EV, sRNA_hen1, sRNA_FBW, RNA-seq, RNA-seq2, RNA-seq_xrn4, PARE, PARE_FBW, PARE_xrn4, MethylC-seq*
MPSS data (obsolete): sRNA & mRNA DGE*
Phyllostachys edulis
Musa acuminata
Hordeum vulgare
Manihot esculenta
Phaseolus vulgaris
Phoenix dactylifera
Lemna gibba
Zea mays (B73)
Mimulus guttatus
Capsicum annuum
Petunia axillaris
Petunia inflata
Populus trichocarpa
Solanum tuberosum
Brassica rapa
Oryza sativa
sRNA, sRNA2, sRNA3, sRNA4, sRNA_ago1d, RNA-seq, RNA-seq_ago1d, PARE, ChIP, mRNA DGE*, MethylC-seq*
MPSS data (obsolete): sRNA & mRNA DGE*
Rosa chinensis
Setaria viridis
Sorghum bicolor
Glycine max
Ustilago maydis
Triticum aestivum
Zostera marina
Our sRNA Tools
Over the years, we have developed a number of tools for plant-centric small RNA analyses. These tools facilitate our work and are key components used in many of our publications. Some are described in publications focused on the tool, and others are unpublished; some are available with a web interface, and some as stand-alone, command-line tools. The links below provide access to these tools, and we hope that you will also find them useful.
PARE Validated miRNA Targets
comPARE
sPARTA
miRNA Similarity Analysis
miRNA Similarity
miRNA Truncation & Tailing Analysis
miTRATA
miRNA Target Prediction
Target Prediction
A prediction web tool identifying potential targets of microRNAs or other small RNAs in the genome or set of sequences chosen or submitted.
miRNA Reverse Target Prediction
Reverse Target Prediction
This tool is useful when no genome is available or when the user wants to assess a specific genomic sequence for targets of small RNAs.
VARNISH
A Special Thanks to the Institutions that Support Our Work
