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miRCarta

Submitted by ChenLiang on Tue, 01/09/2018 - 18:46

The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014.

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sRNATarget

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

Accurate prediction of sRNA targets plays a key role in determining sRNA functions. Here we introduced two mathematical models, sRNATargetNB and sRNATargetSVM, for prediction of sRNA targets using Nai ve Bayes method and support vector machines (SVM), respectively. The training dataset was composed of 46 positive samples (real sRNA-targets interaction) and 86 negative samples (no interaction between sRNA and targets). The leave-one-out cross-validation (LOOCV) classification accuracy was 91.67% for sRNATargetNB, and 100.00% for sRNATargetSVM.

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Average: 5 (1 vote)

miRAFinder and GeneAFinder scripts

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

In recent times, information on miRNAs and their binding sites is gaining momentum. Therefore, there is interest in the development of tools extracting miRNA related information from known literature. Hence, we describe GeneAFinder and miRAFinder scripts (open source) developed using python programming for the semi-automatic extraction and arrangement of updated information on miRNAs, genes and additional data from published article abstracts in PubMed. The scripts are suitable for custom modification as per requirement.

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Average: 5 (1 vote)

miRandb

Submitted by ChenLiang on Mon, 01/09/2017 - 11:45

Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available.

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5
Average: 5 (2 votes)

miTRATA

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

We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online.

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Average: 4.5 (2 votes)

BioVLAB-MMIA

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

MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research.

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Average: 5 (1 vote)

PHMMTSs

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

The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences.

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iScreen

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

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well.

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CePa

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

CePa is an R package aiming to find significant pathways through network topology information. The package has several advantages compared with current pathway enrichment tools. First, pathway node instead of single gene is taken as the basic unit when analysing networks to meet the fact that genes must be constructed into complexes to hold normal functions. Second, multiple network centralities are applied simultaneously to measure importance of nodes from different aspects to make a full view on the biological system.

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Average: 5 (1 vote)

miRseqViewer

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

Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multipanel windows.

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Average: 5 (1 vote)

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