Next-Gen Sequence Databases & sRNA Tools
Produced by the Meyers Lab at the Donald Danforth Plant Science 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


Phyllostachys edulis

Musa acuminata

Manihot esculenta

Phaseolus vulgaris

Phoenix dactylifera

Zea mays (B73)

Mimulus guttatus

Citrus sinensis

Phalaenopsis equestris

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
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

getCRISPR

miRNA Similarity Analysis
miRNA Similarity

miRNA Truncation & Tailing Analysis
miTRATA

sPARTA

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.
