Alignment

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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CentroidAlign – fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

CentroidAlign

The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent findings about functional non-coding RNAs. Recent studies suggest that maximizing the expected accuracy of predictions will be useful for many problems in bioinformatics. Researchers at the Mizuho Information & Research Institute designed a novel estimator for multiple alignments of structured RNAs, based ...

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Increased fraction of novel gene structures for long-noncoding RNAs

Precise identification of RNA-coding regions and transcriptomes of eukaryotes is a significant problem in biology. Currently, eukaryote transcriptomes are analyzed using deep short-read sequencing experiments of complementary DNAs. The resulting short-reads are then aligned against a genome and annotated junctions to infer biological meaning. In this study, scientists at Stanford University use long-read complementary DNA datasets for the analysis of ...

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