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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

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Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions
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Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions

Published on: September 25, 2018

Probability-based shotgun cross-linking sites analysis.

Young Jin Lee1

  • 1Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA. yjlee@iastate.edu

Journal of the American Society for Mass Spectrometry
|August 12, 2009
PubMed
Summary
This summary is machine-generated.

We enhanced X!Link, a tool for analyzing cross-linked proteins, with a new scoring system. This system uses E-values to accurately detect cross-links and minimize false positives in protein sequence analysis.

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Area of Science:

  • Proteomics
  • Biochemistry
  • Computational Biology

Background:

  • Accurate analysis of chemically cross-linked proteins and multiprotein complexes is crucial for understanding protein interactions.
  • Previous methods, like the initial X!Link tool, faced challenges with high-throughput analysis and minimizing false positives.

Purpose of the Study:

  • To improve the X!Link tool for cross-linking site analysis by implementing a probability-based scoring system.
  • To enhance the sensitivity and reduce false positives in the detection of cross-linked peptides.
  • To enable the application of the tool to moderate numbers of protein sequences.

Main Methods:

  • Development of a probability-based scoring system incorporating explicit E-values.
  • Calculation of additional E-values for individual peptides to address partial matching issues.
  • Application of the enhanced X!Link tool to a dataset of cross-linked cytochrome c.

Main Results:

  • The new scoring system enables sensitive detection of cross-links with very low false positives.
  • Additional E-value calculations effectively minimized false positives arising from partial peptide matching.
  • The enhanced tool demonstrated its utility in analyzing cross-linked proteins against large sequence databases.

Conclusions:

  • The improved X!Link tool with a probability-based scoring system significantly enhances the accuracy of cross-linking site analysis.
  • The system is capable of sensitive detection of cross-links, even with moderate numbers of protein sequences.
  • This advancement facilitates more reliable identification of protein interactions through chemical cross-linking studies.