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siDRM

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

Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool.

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RNAither

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

We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for data normalization, different statistical tests for the identification of significant siRNAs, and a significance analysis of the biological processes involving corresponding genes.

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PatMaN

Submitted by ChenLiang on Sun, 09/10/2017 - 20:06

We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed.

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miRGate

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

MicroRNAs (miRNAs) are small non-coding elements involved in the post-transcriptional down-regulation of gene expression through base pairing with messenger RNAs (mRNAs). Through this mechanism, several miRNA-mRNA pairs have been described as critical in the regulation of multiple cellular processes, including early embryonic development and pathological conditions. Many of these pairs (such as miR-15b/BCL2 in apoptosis or BART-6/BCL6 in diffuse large B-cell lymphomas) were experimentally discovered and/or computationally predicted.

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GeneCodis

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

We present GENECODIS, a web-based tool that integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by statistical significance. The analysis of concurrent annotations provides significant information for the biologic interpretation of high-throughput experiments and may outperform the results of standard methods for the functional analysis of gene lists.

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Chipster

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

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software.

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CPSS

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

Next generation sequencing (NGS) techniques have been widely used to document the small ribonucleic acids (RNAs) implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analysing the enormous datasets from small RNA deep sequencing approach.

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CleaveLand

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

MicroRNAs (miRNAs) are approximately 20- to 22-nt long endogenous RNA sequences that play a critical role in the regulation of gene expression in eukaryotic genomes. Confident identification of miRNA targets is vital to understand their functions. Currently available computational algorithms for miRNA target prediction have diverse degrees of sensitivity and specificity and as a consequence each predicted target generally requires experimental confirmation.

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Average: 5 (1 vote)

isomiRex

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

We present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets.

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The UEA sRNA workbench

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

RNA silencing is a complex, highly conserved mechanism mediated by small RNAs (sRNAs), such as microRNAs (miRNAs), that is known to be involved in a diverse set of biological functions including development, pathogen control, genome maintenance and response to environmental change. Advances in next generation sequencing technologies are producing increasingly large numbers of sRNA reads per sample at a fraction of the cost of previous methods.

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