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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
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Published on: December 2, 2009

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Stefan Washietl1, Sven Findeiss, Stephan A Müller

  • 1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB101SD, United Kingdom. wash@mit.edu

RNA (New York, N.Y.)
|March 2, 2011
PubMed
Summary
This summary is machine-generated.

RNAcode identifies coding regions in RNA sequences using a novel statistical model. This tool aids in discovering new short peptides and analyzing RNA coding potential across all life domains.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Distinguishing coding from noncoding RNAs is crucial with increasing genomic data.
  • Existing gene-finding software has limitations for emerging applications.

Purpose of the Study:

  • To introduce RNAcode, a novel program for detecting coding regions in multiple sequence alignments.
  • To address limitations of current gene-finding software for new applications.

Main Methods:

  • RNAcode employs a unified statistical model integrating nucleotide substitution and gap patterns.
  • The algorithm handles real-world data issues like alignment and sequencing errors.
  • It requires no training, making it applicable across all domains of life.

Main Results:

  • RNAcode successfully predicted and confirmed seven novel short peptides in Escherichia coli.
  • Analysis of previously noncoding RNAs revealed their coding potential.
  • The software is open-source and available for major platforms.

Conclusions:

  • RNAcode offers a robust, versatile tool for identifying coding RNA regions.
  • It facilitates the discovery of novel peptides and re-evaluation of RNA function.
  • The method advances the analysis of genomic and transcriptomic data.