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Related Concept Videos

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.
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Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Ribozymes02:47

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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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taveRNA: a web suite for RNA algorithms and applications.

Cagri Aksay1, Raheleh Salari, Emre Karakoc

  • 1Lab for Computational Biology, SFU, Canada.

Nucleic Acids Research
|May 10, 2007
PubMed
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taveRNA offers three RNA web services for predicting RNA secondary structures, RNA-RNA interactions, and identifying potential ncRNA regulators. These tools enhance RNA bioinformatics by providing efficient and accurate computational solutions.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA structure and interactions are crucial for biological functions.
  • Predicting RNA secondary structures and RNA-RNA interactions is computationally challenging.
  • Identifying regulatory ncRNAs requires efficient database searching.

Purpose of the Study:

  • Introduce taveRNA, a web server package integrating three novel RNA web services.
  • Provide advanced tools for RNA secondary structure prediction (alteRNA).
  • Enable prediction of RNA-RNA interaction structures (inteRNA) and efficient ncRNA database pruning (pRuNA).

Main Methods:

  • alteRNA utilizes dynamic programming to minimize energy density and free energy for RNA secondary structure prediction.
  • inteRNA employs dynamic programming to minimize free energy for joint RNA-RNA interaction structure prediction.
  • pRuNA uses a database pruning approach to identify potential ncRNA regulators.

Main Results:

  • Developed alteRNA, a novel RNA secondary structure prediction tool.
  • Launched inteRNA, the first web service for RNA-RNA interaction structure prediction.
  • Implemented pRuNA for efficient ncRNA database searching and identification of potential regulators.

Conclusions:

  • taveRNA provides a comprehensive suite of tools for RNA structure and interaction analysis.
  • The integrated services offer significant advancements in RNA bioinformatics.
  • taveRNA is accessible via a web server, facilitating broader research applications.