Sticking with the theme of plant RNA analysis, (can’t help it, we’re attending the Plant and Animal Genomes Conference this week and have plants on the brain) here is a great set of tools developed by the The Zhao Bioinformatics Laboratory at the Noble Foundation. Some of the goals of this project are:
- to develop graphical models to model and simulate plant transcriptional regulatory networks;
- to develop novel computational algorithms to infer large-scale gene regulatory networks (GRNs) from high throughput functional genomics data in model plants;
Their central methods involve (1) modeling and simulation of genome-scale associations, including causal relationships, among key regulatory elements such as genes, functional non-coding RNAs, proteins, metabolites, signaling components and other emergent properties using graphical models; (2) novel informatics for discovering and inferring large-scale gene regulatory networks from high throughput Microarray based and RNA-Seq based gene expression data, and (3) system and data integration to elucidate networks.
iPlantTF – integrates 1) a sophisticate back-end high-performance parallel computing prediction module to systematically identify and classify plant transcription factors in user-submitted sequences at very high prediction accuracy and coverage, and 2) a series of intuitive web interfaces for user to submit large-scale sequences and retrieve analysis results.
Target Gene & Promoter Analysis – a novel systematic computational approach for predicting TFTGs directly on a genome scale.
pssRNAMiner: a plant short small RNA regulatory cascade analysis server which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.
psRNATarget: a plant small RNA target analysis server which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA.
LegumeIP – an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes