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Python is a widely used high-level, general-purpose, interpreted, dynamic programming language. [Source: Wikipedia ]

De Novo SVM Classification of Precursor MicroRNAs

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

MicroRNAs (miRNAs) are small ncRNAs participating in diverse cellular and physiological processes through the post-transcriptional gene regulatory pathway. Critically associated with the miRNAs biogenesis, the hairpin structure is a necessary feature for the computational classification of novel precursor miRNAs (pre-miRs). Though many of the abundant genomic inverted repeats (pseudo hairpins) can be filtered computationally, novel species-specific pre-miRs are likely to remain elusive.

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miREnvironment

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

The interaction between genetic factors and environmental factors has critical roles in determining the phenotype of an organism. In recent years, a number of studies have reported that the dysfunctions on microRNA (miRNAs), environmental factors and their interactions have strong effects on phenotypes and even may result in abnormal phenotypes and diseases, whereas there has been no a database linking miRNAs, environmental factors and phenotypes.

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Empirical GO

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

Many studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional categories, many of which appear frequently in the analysis of apparently unrelated diseases and conditions.

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SHRiMP

Submitted by ChenLiang on Thu, 04/06/2017 - 19:08

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism.

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TAM

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

MicroRNAs (miRNAs) are a class of important gene regulators. The number of identified miRNAs has been increasing dramatically in recent years. An emerging major challenge is the interpretation of the genome-scale miRNA datasets, including those derived from microarray and deep-sequencing. It is interesting and important to know the common rules or patterns behind a list of miRNAs, (i.e. the deregulated miRNAs resulted from an experiment of miRNA microarray or deep-sequencing).

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DARIO

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

Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investigate the entire ncRNAome in an essentially unbiased way. However, there is a substantial need for methods that allow a convenient analysis of these overwhelmingly large data sets. Here, we present DARIO, a free web service that allows to study short read data from small RNA-seq experiments.

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omiRas

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

Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few.

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CAP-miRSeq

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

miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant amount of computational resources and bioinformatics expertise. Several web based analytical tools have been developed but they are limited to processing one or a pair of samples at time and are not suitable for a large scale study.

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MirSNP

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

Numerous single nucleotide polymorphisms (SNPs) associated with complex diseases have been identified by genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs) studies. However, few of these SNPs have explicit biological functions. Recent studies indicated that the SNPs within the 3'UTR regions of susceptibility genes could affect complex traits/diseases by affecting the function of miRNAs. These 3'UTR SNPs are functional candidates and therefore of interest to GWAS and eQTL researchers.

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CID-miRNA

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

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes.

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