Next-Gen Sequence Databases & sRNA Tools

Produced by the Meyers Lab at the UC Davis Genome Center


DatabasessRNA Tools

About Us

Lab icon

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.

Featured publication from our lab

Zhan et al., PNAS (2024)
Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in
biogenesis mechanism and molecular function

Featured publication from our lab

Zhan et al., Annual Review of Plant Biology (2023)
Plant small RNAs: their biogenesis, regulatory roles, and functions

Featured publication from our lab

Bélanger et al., The Plant Cell (2023)
Plastid dsRNA transgenes trigger phased small RNA-based gene silencing of
nuclear-encoded genes

Featured publication from our lab

Pokhrel et al., Nat Commun (2021)
Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants

Our Databases

Database icon

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.




Click the “+” sign to show database links for each organism.  
Note:  Those links marked with “*” are excluded from the database and library totals above.

Amborella logo
Amborella trichopoda
Apple logo
Malus domestica
Asparagus logo
Asparagus officinalis
Bamboo logo
Phyllostachys edulis
Banana logo
Musa acuminata
Brachypodium logo
Brachypodium distachyon
Cassava logo
Manihot esculenta
Columbine logo
Aquilegia coerulea
Common bean logo
Phaseolus vulgaris
Date palm logo
Phoenix dactylifera
Medicago logo
Solanum melongena
Flax logo
Linum usitatissimum
Chicken logo
Gallus gallus
Grape logo
Vitis vinifera

sRNA_Atlas, sRNA_GxE

MPSS data (obsolete): mRNA DGE*

Magnaporthe logo
Magnaporthe oryzae

sRNA, RNA-seq

MPSS data (obsolete): mRNA DGE*

Medicago logo
Medicago truncatula
Mimulus logo
Mimulus guttatus
Mimulus logo
Nicotiana benthamiana
Orange logo
Citrus sinensis
Orchid logo
Phalaenopsis equestris
Papaya logo
Carica papaya
Peach logo
Prunus persica
Petunia ax. logo
Capsicum annuum
Petunia ax. logo
Petunia axillaris
Petunia in. logo
Petunia inflata
Pineapple logo
Ananas comosus
Poplar logo
Populus trichocarpa
Potato logo
Solanum tuberosum
Rapa logo
Brassica rapa
Rice brachyantha logo
Oryza brachyantha
Rice glaberrima logo
Oryza glaberrima
Rice logo
Oryza punctata
Rice puncata logo
Oryza sativa
Rose logo
Rosa chinensis
Setaria logo
Setaria viridis
Sorghum logo
Sorghum bicolor
Spirodela logo
Spirodela polyrhiza
Strawberry logo
Fragaria ananassa
Streptpchaeta logo
Streptochaeta angustifolia
Tauschii logo
Aegilops tauschii
Zostera logo
Nicotiana tabacum
Tomato logo
Solanum lycopersicum
Ustilago logo
Ustilago maydis
Wheat logo
Triticum aestivum
Zostera logo
Zostera marina

Our sRNA Tools

Tool icon

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.

Orange pic

PARE Validated miRNA Targets


A web resource for exploring miRNA-target interactions validated by PARE data. See Kakrana et al. (2014) Nucleic Acids Research.
Leaf pic
Small RNA-PARE Targets Analyzer


A high performance software for the validation of plant miRNA or sRNA targets with PARE data. See Kakrana et al. (2014) Nucleic Acids Research.
Grape pic

miRNA Similarity Analysis

miRNA Similarity

This web tool is useful for comparisons of small RNA sequences to rapidly find near matches or homologs of microRNAs and other plant small RNAs.
Lettuce pic

miRNA Truncation & Tailing Analysis


The first web-based tool for the analysis of 3’ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. See Patel et al. (2015) Bioinformatics.
Tomato pic

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.

Leaf pic

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.

Leaf pic
Vetting & Analysis of RNA for In Situ Hybridization


An online software tool for designing probes used for super resolution imaging of RNAs with Points Accumulation for Imaging in Nanoscale Topography (RNA-PAINT). See Huang et al. (2020) Nucleic Acids Research.

A Special Thanks to the Institutions that Support Our Work

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DatabasessRNA Tools