piRNA
Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact.
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Other Species
A personalized microRNA microarray normalization method using a logistic regression model
MicroRNA (miRNA) is a set of newly discovered non-coding small RNA molecules. Its significant effects have contributed to a number of critical biological events including cell proliferation, apoptosis development, as well as tumorigenesis. High-dimensional genomic discovery platforms (e.g. microarray) have been employed to evaluate the important roles of miRNAs by analyzing their expression profiling.
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miREval
We have developed an online tool called mirEval which can search sequences of up to 10 000 nt for novel microRNAs in multiple organisms. It is a comprehensive tool, easy to use and very informative. It will allow users with no prior knowledge of in-silico detection of microRNAs to take advantage of the most successful approaches to investigate sequences of interest.
The mirEval web server is available at http://tagc.univ-mrs.fr/mireval[1]
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RNAiDB
RNA interference (RNAi) is being used in large-scale genomic studies as a rapid way to obtain in vivo functional information associated with specific genes. How best to archive and mine the complex data derived from these studies provides a series of challenges associated with both the methods used to elicit the RNAi response and the functional data gathered. RNAiDB (RNAi Database; http://www.rnai.org) has been created for the archival, distribution and analysis of phenotypic data from large-scale RNAi analyses in Caenorhabditis elegans.
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Oasis
Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs.
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sRNAtoolbox
Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates.
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wapRNA
mRNA/miRNA-seq technology is becoming the leading technology to globally profile gene expression and elucidate the transcriptional regulation mechanisms in living cells. Although there are many tools available for analyzing RNA-seq data, few of them are available as easy accessible online web tools for processing both mRNA and miRNA data for the RNA-seq based user community. As such, we have developed a comprehensive web application tool for processing mRNA-seq and miRNA-seq data.
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Chimira
Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g.
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miRBase Tracker
Since 2002, information on individual microRNAs (miRNAs), such as reference names and sequences, has been stored in miRBase, the reference database for miRNA annotation. As a result of progressive insights into the miRNome and its complexity, miRBase underwent addition and deletion of miRNA records, changes in annotated miRNA sequences and adoption of more complex naming schemes over time.
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siDesign
One critical step in RNA interference (RNAi) experiments is to design small interfering RNAs (siRNAs) that can greatly reduce the expression of the target transcripts, but not of other unintended targets. Although various statistical and computational approaches have been attempted, this remains a challenge facing RNAi researchers. Here, we present a new experimentally validated method for siRNA design.
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