Annotation

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

lncrna

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, current reference gene collections remain far from complete: many genes models are fragmentary, while thousands more remain uncatalogued, particularly for long non coding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture ...

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FEELnc – a tool for long non-coding RNA annotation

lncRNA

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, researchers from University Rennes1 present FEELnc (FlExible Extraction of ...

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AnnoLnc – a web server for systematically annotating novel human lncRNAs

lncRNA

Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here researchers from Peking University present AnnoLnc, a one-stop portal for systematically annotating novel human ...

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Structural and Functional Annotation of Long Noncoding RNAs

lncrna

Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, ...

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LDAP – a web server for lncRNA-disease association prediction

lncRNA

Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. Researchers at Central South University, ...

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CHART – Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets

lncRNA

Capture Hybridization Analysis of RNA Targets (CHART) has recently been developed to map the genome-wide binding profile of chromatin-associated RNAs. This protocol uses a small number of 22-28 nucleotide biotinylated antisense oligonucleotides, complementary to regions of the target RNA that are accessible for hybridization, to purify RNAs from a cross-linked chromatin extract. RNA-chromatin complexes are next immobilized on beads, washed, ...

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COME – a robust coding potential calculation tool for lncRNA identification and characterization

lncrna

Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, researchers at Tsinghua University have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose-compose method, which ...

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Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer

lncRNA

Multiple computational tools have been widely applied to the detection of coding driver mutations in cancer; however, the prioritization of pathogenic non-coding variants remains a difficult and demanding task. The present study was performed to distinguish non-coding disease-causing mutations from neutral ones, and to prioritize potential cancer-associated long non-coding RNAs (lncRNAs) with a logistic regression model in lung cancer. A ...

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FMLNCSIM – fuzzy measure-based lncRNA functional similarity calculation model

lncRNA

Accumulating experimental studies have indicated the influence of lncRNAs on various critical biological processes as well as disease development and progression. Calculating lncRNA functional similarity is of high value in inferring lncRNA functions and identifying potential lncRNA-disease associations. However, little effort has been attempt to measure the functional similarity among lncRNAs on a large scale. Now, researchers have developed a ...

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lncRNATargets – A platform for lncRNA target prediction based on nucleic acid thermodynamics

lncRNA

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. Researchers at the Peking Union Medical College have developed  lncRNATargets, which is a web-based platform for ...

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