Next-Gen Sequence Databases & sRNA Tools
Produced by the Meyers Lab at the UC Davis Genome Center
About Us
![Lab icon Lab icon](https://mpss.meyerslab.org/wp-content/uploads/2020/06/favicon-1024x1024-1.png)
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
![Database icon Database icon](https://mpss.meyerslab.org/wp-content/uploads/2020/07/30351205.png)
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.
![Apple logo Apple logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-2.png)
Malus domestica
![Arabidopsis logo Arabidopsis logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-3.png)
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*
![Bamboo logo Bamboo logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-5.png)
Phyllostachys edulis
![Banana logo Banana logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-6.png)
Musa acuminata
![Barley logo Barley logo](https://mpss.meyerslab.org/wp-content/uploads/2020/12/logo.png)
Hordeum vulgare
![Cassava logo Cassava logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-9.png)
Manihot esculenta
![Common bean logo Common bean logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-11.png)
Phaseolus vulgaris
![Date palm logo Date palm logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-12.png)
Phoenix dactylifera
![Lemna logo Lemna logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-14.png)
Lemna gibba
![Maize logo Maize logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-18.png)
Zea mays (B73)
![Mimulus logo Mimulus logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-20.png)
Mimulus guttatus
![logo Petunia ax. logo](https://mpss.meyerslab.org/wp-content/uploads/2024/05/logo-5.png)
Capsicum annuum
![Petunia ax. logo Petunia ax. logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-25.png)
Petunia axillaris
![Petunia in. logo Petunia in. logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-26.png)
Petunia inflata
![Poplar logo Poplar logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-28.png)
Populus trichocarpa
![Potato logo Potato logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-29.png)
Solanum tuberosum
![Rapa logo Rapa logo](https://mpss.meyerslab.org/wp-content/uploads/2021/03/logo.png)
Brassica rapa
![Rice puncata logo Rice puncata logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-31.png)
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*
![Rose logo Rose logo](https://mpss.meyerslab.org/wp-content/uploads/2021/08/logo-1.png)
Rosa chinensis
![Setaria logo Setaria logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-32.png)
Setaria viridis
![Sorghum logo Sorghum logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-33.png)
Sorghum bicolor
![Soybean logo Soybean logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-34.png)
Glycine max
![Ustilago logo Ustilago logo](https://mpss.meyerslab.org/wp-content/uploads/2021/03/logo-1.png)
Ustilago maydis
![Wheat logo Wheat logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-40.png)
Triticum aestivum
![Zostera logo Zostera logo](https://mpss.meyerslab.org/wp-content/uploads/2020/07/logo-41.png)
Zostera marina
Our sRNA Tools
![Tool icon Tool icon](https://mpss.meyerslab.org/wp-content/uploads/2020/07/meyers_icon.png)
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 from https://www.pexels.com/photo/photo-of-pile-of-oranges-2294477/ Orange pic](https://mpss.meyerslab.org/wp-content/uploads/2020/07/photo-of-pile-of-oranges-2294477-1-scaled.jpg)
PARE Validated miRNA Targets
comPARE
![Leaf pic rom https://www.pexels.com/photo/closeup-photo-of-sprout-1002703/ Leaf pic](https://mpss.meyerslab.org/wp-content/uploads/2020/07/leaf.png)
sPARTA
![Grape pic from https://www.pexels.com/photo/grapes-vineyard-vine-purple-grapes-39511/ Grape pic](https://mpss.meyerslab.org/wp-content/uploads/2020/07/grapes.png)
miRNA Similarity Analysis
miRNA Similarity
![Lettuce pic from https://www.pexels.com/photo/close-up-photo-of-green-leafed-plants-1213859/ Lettuce pic](https://mpss.meyerslab.org/wp-content/uploads/2020/07/lettuce.png)
miRNA Truncation & Tailing Analysis
miTRATA
![Tomato pic from https://www.pexels.com/photo/tomatoes-1367242/ Tomato pic](https://mpss.meyerslab.org/wp-content/uploads/2020/07/tomatoes.png)
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.
![pexels-ave-calvar-martinez-6944172 Leaf pic](https://mpss.meyerslab.org/wp-content/uploads/2023/04/pexels-ave-calvar-martinez-6944172-scaled-e1681525430872.jpg)
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.
![orchid Leaf pic](https://mpss.meyerslab.org/wp-content/uploads/2020/10/orchid.jpg)