Arabidopsis RNA-seq Database

Search gene expression levels from 20,000+ public Arabidopsis RNA-Seq libraries

CyVerse Learning Centre for RNAseq analysis

Tutorials are focused not just on how to conduct analyses with CyVerse tools, but also on communicating best practices that help users apply computational thinking and avoid common bioinformatics pitfalls.

 Tutorials cover popular science topics such as how to use RNA-Seq to study differential gene expression, and how to use genome-wide association studies (GWAS) to identify genes and controlling elements associated with specific traits.

NEB RNA Analysis Tools

RNA Analysis includes these areas of focus:


- Cappable-seq

- In vitro Synthesis (IVT)

- RNA Labeling

- RNA Modification

- RNA Purification and Isolation

- RNA-seq

- RT-qPCR, RT-PCR and cDNA Synthesis

- Small RNA Detection and Isolation



PsRobot: Plant small RNA analysis toolbox

PsRobot is designed to analyze batch of plant small RNA data. The online version of psRobot has two modules:

The stem-loop small RNA prediction (try it out) module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences.

The second module, small RNA target prediction (try it out) module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants.


The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.

RNA sequencing analysis software tools

RNA sequencing (RNA-seq) also known as whole transcriptome shotgun sequencing (WTSS) is the next-generation sequencing technology to study the transcriptome. It could be used as an alternative to microarrays for gene expression analysis, without the need to know the RNA sequence a priori. RNA-seq offers more accurate data and applications including detection of gene fusion, variants, alternative splicing, post-transcriptional modifications as well as for analysis of small RNAs such as tRNA or miRNA profiles.

A complete picture of the RNA content can be obtained from low quantity biological samples. Several analytical steps are critical for a successful characterization and quantification of the transcriptome. A large list of bioinformatic tools is proposed here for quality control, data processing, quantification, annotation and visualization as well as for interpretation and biological network analysis for understanding RNA-seq data.


A stand-alone software tool developed by the NCBI for submitting and updating entries to public sequence databases (GenBank, EMBL, or DDBJ). It is capable of handling simple submissions that contain a single short mRNA sequence, complex submissions containing long sequences, multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments