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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...
Improving Translational Accuracy02:07

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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...
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Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Fixing Double-strand Breaks

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Related Experiment Video

Updated: May 8, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Adjusting scoring matrices to correct overextended alignments.

Lauren J Mills1, William R Pearson

  • 1Department of Molecular, Cell and Developmental Biology and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

Bioinformatics (Oxford, England)
|September 3, 2013
PubMed
Summary
This summary is machine-generated.

Sequence similarity searches using standard scoring matrices can overextend alignments, especially for closely related sequences. Adjusting matrices based on sequence identity significantly improves alignment accuracy, correcting overextended boundaries.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Related Experiment Videos

Last Updated: May 8, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Sequence similarity searches are crucial for identifying homologous proteins.
  • Standard scoring matrices like BLOSUM62 are optimized for low-identity alignments, aiding distant homolog detection.
  • These matrices can lead to overextended local alignments, including non-homologous regions.

Purpose of the Study:

  • To evaluate the accuracy of local alignment boundaries in BLASTP and SSEARCH.
  • To investigate the causes of overextended alignments.
  • To develop a method for improving alignment accuracy by adjusting scoring matrices.

Main Methods:

  • Assessed alignment boundary accuracy using a benchmark dataset with known correct boundaries.
  • Analyzed the frequency and characteristics of overextended alignments.
  • Developed a method to predict optimal scoring matrices based on sequence identity.
  • Realigned sequences using predicted scoring matrices.

Main Results:

  • 7% of BLASTP and 8% of SSEARCH alignments showed overextended boundaries.
  • Overextension was more common in higher-identity alignments (>33%).
  • Adjusting scoring matrices to match sequence identity corrected overextended boundaries.
  • Predicting and using identity-specific matrices corrected 37% of overextended alignments.

Conclusions:

  • Standard scoring matrices can produce inaccurate local alignments, particularly for closely related sequences.
  • A novel approach of predicting and applying identity-specific scoring matrices substantially improves alignment accuracy.
  • This method offers a more reliable way to define homologous regions in sequence similarity searches.