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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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The SEQUEST family tree.

David L Tabb1

  • 1School of Medicine, Vanderbilt University, Nashville, TN, 37232-8575, USA. david.l.tabb@vanderbilt.edu.

Journal of the American Society for Mass Spectrometry
|July 1, 2015
PubMed
Summary
This summary is machine-generated.

The SEQUEST algorithm has evolved significantly since 1994, incorporating new features and inspiring successor tools. Advances in computing power and mass spectrometry have driven these improvements, creating a diverse SEQUEST family.

Keywords:
BioinformaticsHistoryIntellectual propertyProteomicsSEQUEST

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The SEQUEST algorithm, developed in 1994, is a foundational tool in proteomics data analysis.
  • Its success has led to the development of numerous successor algorithms and ongoing research.
  • Understanding its evolution is crucial for interpreting modern mass spectrometry data.

Purpose of the Study:

  • To provide an account and perspective on the evolution of the SEQUEST algorithm.
  • To map the development of SEQUEST and its related contributions.
  • To highlight the diversity within the SEQUEST algorithm family.

Main Methods:

  • Review of historical contributions and advancements in SEQUEST.
  • Analysis of the impact of computing improvements (clusters, GPUs) on algorithm speed.
  • Examination of how mass spectrometry innovations (mass accuracy, activation methods) influenced fragment modeling and scoring.

Main Results:

  • SEQUEST has gained substantial new capabilities since its inception.
  • Numerous successor algorithms have built upon the original SEQUEST framework.
  • Improvements in computing speed and mass spectrometry techniques have been key drivers of evolution.
  • Significant diversity exists among the various "SEQUEST family" members.

Conclusions:

  • The SEQUEST algorithm's legacy is marked by continuous innovation and adaptation.
  • The interplay between computational power and mass spectrometry technology has shaped its development.
  • The SEQUEST family represents a rich and diverse set of tools for proteomics research.