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Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Extraction: Advanced Methods00:56

Extraction: Advanced Methods

Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is formed in...

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Related Experiment Video

Updated: Jun 10, 2026

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

Text mining meets workflow: linking U-Compare with Taverna.

Yoshinobu Kano1, Paul Dobson, Mio Nakanishi

  • 1Department of Computer Science, The University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan. kano@is.s.u-tokyo.ac.jp

Bioinformatics (Oxford, England)
|August 17, 2010
PubMed
Summary

Bioinformatics researchers can now easily create and run text mining workflows using the U-Compare system, which integrates with Taverna for enhanced accessibility and interoperability of bio text mining resources.

Related Experiment Videos

Last Updated: Jun 10, 2026

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Text Mining

Background:

  • Text mining of biomedical literature is crucial but challenging for bioinformaticians.
  • Existing text mining resources lack accessibility and interoperability.
  • Developing and executing text mining workflows requires coding expertise.

Purpose of the Study:

  • To enhance accessibility and interoperability of bio text mining resources.
  • To enable easy creation, execution, evaluation, and visualization of text mining workflows without coding.
  • To integrate the U-Compare system with the Taverna workflow system.

Main Methods:

  • The U-Compare system was developed to provide a comprehensive suite of bio text mining tools.
  • Workflows were designed to be highly interoperable within the U-Compare environment.
  • U-Compare was linked to Taverna, a generic workflow management system.

Main Results:

  • U-Compare offers a user-friendly, no-code environment for building and running text mining workflows.
  • The integration with Taverna exposes U-Compare's text mining capabilities to a wider bioinformatics community.
  • Workflows can be easily created, executed, evaluated, and visualized.

Conclusions:

  • The U-Compare system, integrated with Taverna, significantly improves the accessibility and usability of bio text mining resources.
  • Bioinformaticians can now leverage powerful text mining tools without extensive programming knowledge.
  • This facilitates more efficient analysis of biomedical literature.