University of California, Berkeley | Plant & Microbial Biology
SoMART Webserver for miRNA & siRNA Analysis
We designed the SoMART webserver with a suite of bioinformatic tools and sequence databases for discovery and analyses of miRNAs and siRNAs that regulate plant genes of interest.
Use SoMART (Solanaceae miRNA/tasiRNA Analysis Resources and Tools) programs below to: identify miRNAs and siRNAs targeting a gene of interest, detect miRNA/siRNA cleaved transcripts, identify miRNA/siRNA progenitors, map small RNAs to progenitor sequences and confirm miRNA/siRNA targets.
Slicer Detector
Detect small RNAs that can potentially target your gene of interest from sRNA-seq libraries
in potato, tomato, and tobacco.
dRNA mapper
The degradome RNA-seq (dRNA-seq) library from wild type potato, tomato, and tobacco
are available for detecting cleavage product from your gene of interest.
preMIR detector
Detect genetic loci or precursor sequences of your input small RNA and determine if
they can fold into MIR structures.
sRNA Mapper
The small RNA (sRNA-seq) libraries from potato, tomato, and tobacco are available for
detecting and mapping sRNAs produced from your gene of interest in each species.
SMART COMPARE
Compare results from Slicer Detector and dRNA mapper and Identify slicers supported by
dRNA reads mapped to predicted cleavage site.
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If you generate data for your publication with this server, please cite:
Li F, Orban R, Baker B (2012) SoMART: a web server for plant miRNA, tasiRNA and target
gene analysis. Plant J 70: 891-901. Download PDF
Public databases generated from others' work are used for SoMart.
To cite these data sources, please refer to database descriptions in Table S1.
If you want analyze your own databases, please contact Feng Li or Barbara Baker
(email:lifeng@berkeley.edu, bbaker@berkeley.edu) and send your data in a tab-delimited
two-column list format with read sequence followed by read number (eg: AGCTGACGATTACA 200)
in a DVD or CD.