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Inchworm assembles the RNA-Seq data into transcript sequences, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts. Chrysalis clusters the Inchworm contigs and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full ...
Currently RNA-Seq relies on copying RNA molecules into cDNA molecules prior to sequencing; therefore, the subsequent platforms are the same for transcriptomic and genomic data. Consequently, the development of DNA sequencing technologies has been a defining feature of RNA-Seq. [ 78 ] [ 80 ] [ 81 ] Direct sequencing of RNA using nanopore ...
The binding of the ADAR2 enzyme to the RNA timestamp initiates the gradual conversion of adenosine to inosine molecules. Over time, these edits accumulate and are then read through RNA-seq. This technology allows us to glean cell-type specific temporal information associated with RNA-seq data, that until now, has not been accessible. [1]
De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome.These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes.
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome. [2] [3]
queryable-rna-seq-database Formally known as the Queryable RNA-Seq Database, this system is designed to simplify the process of RNA-seq analysis by providing the ability upload the result data from RNA-Seq analysis into a database, store it, and query it in many different ways.
Both methods attempt to generate biologically representative isoform-level constructs from RNA-seq data and generally attempt to associate isoforms with a gene-level construct. However, proper identification of gene-level constructs may be complicated by recent duplications, paralogs, alternative splicing or gene fusions. These complications ...
RNA Seq Experiment. The single-cell RNA-seq technique converts a population of RNAs to a library of cDNA fragments. These fragments are sequenced by high-throughput next generation sequencing techniques and the reads are mapped back to the reference genome, providing a count of the number of reads associated with each gene. [13]