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siRNA Design Software

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs.

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siRNArules

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNAi interference and siRNA have become useful tools for investigation of gene function. However, the discovery that not all siRNA are equally efficient made necessary screens or design algorithms to obtain high activity siRNA candidates. Several algorithms have been published, but they remain inefficient, obscure, or commercially restricted. This article describes an open-source JAVA program that is surprisingly efficient at predicting active siRNAs (Pearson correlation coefficient r = 0.52, n = 526 siRNAs).

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HCS-Analyzer

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

High-throughput screening is a powerful technology principally used by pharmaceutical industries allowing the identification of molecules of interest within large libraries. Originally target based, cellular assays provide a way to test compounds (or other biological material such as small interfering RNA) in a more physiologically realistic in vitro environment. High-content screening (HCS) platforms are now available at lower cost, giving the opportunity for universities or research institutes to access those technologies for research purposes.

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miRNAminer

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental and computational methods were used to construct miRNA gene repositories agreeing with careful submission guidelines.

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miRNEST

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs.

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piRNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

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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MiRFinder

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them.

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A personalized microRNA microarray normalization method using a logistic regression model

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

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

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

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

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

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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