Tag Archives: Annotation

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

lncrna

Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines ...

Read More »

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 ...

Read More »

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 ...

Read More »

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 ...

Read More »

Discovery and annotation of long noncoding RNAs

lncRNA

Recent advances in RNA-sequencing technologies have led to the discovery of thousands of previously unannotated noncoding transcripts, including many long noncoding RNAs (lncRNAs) whose functions remain largely unknown. Discussed here are considerations and best practices in lncRNA identification and annotation, which we hope will foster functional and mechanistic exploration. Perhaps the biggest surprise of the postgenomic era has been the ...

Read More »

lncRNAtor – Functional Investigation of long noncoding RNAs

lncRNAtor aims to be the lncRNA (long non-coding RNA) portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were collected from TCGA, GEO, ENCODE, and modENCODE (Organism: Human, Mouse, Fly, Worm, and Yeast). Our system workflow is shown below. lncRNAtor is preparing to submit a paper. (2013.06.03)

Read More »

lncRNAtor – Functional Investigation of long noncoding RNAs

lncRNAtor aims to be the lncRNA (long non-coding RNA) portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were collected from TCGA, GEO, ENCODE, and modENCODE (Organism: Human, Mouse, Fly, Worm, and Yeast). Our system workflow is shown below. lncRNAtor is preparing to submit a paper. (2013.06.03)

Read More »

Systematically profiling and annotating long intergenic non-coding RNAs

While more and more long intergenic non-coding RNAs (lincRNAs) were identified to take important roles in both maintaining pluripotency and regulating differentiation, how these lincRNAs may define and drive cell fate decisions on a global scale are still mostly elusive. Systematical profiling and comprehensive annotation of embryonic stem cells lincRNAs may not only bring a clearer big picture of these ...

Read More »