Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.

Aaron J Mackey1, Timothy A J Haystead, William R Pearson

  • 1Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA.

Molecular & Cellular Proteomics : MCP
|July 4, 2002
PubMed
Summary

Two new algorithms, FASTS and FASTF, identify homologous sequences using multiple short peptides. These tools enable proteomic identification from organisms with unsequenced genomes, even for ancient divergences.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Development of domain-specific probes of <i>Plasmodium falciparum</i> heat shock protein 70-1.

Antimicrobial agents and chemotherapy·2026
Same author

An Inhibitor of Death-Associated Protein Kinase 3 (DAPK3) Disrupts Hippo Signaling and Intestinal Epithelial Regeneration in Murine DSS-Induced Colitis.

Digestive diseases and sciences·2025
Same author

Improved selection of canonical proteins for reference proteomes.

NAR genomics and bioinformatics·2024
Same author

Cooperative involvement of zipper-interacting protein kinase (ZIPK) and the dual-specificity cell-division cycle 14A phosphatase (CDC14A) in vascular smooth muscle cell migration.

bioRxiv : the preprint server for biology·2024
Same author

Selective targeting of Plasmodium falciparum Hsp90 disrupts the 26S proteasome.

Cell chemical biology·2024
Same author

Targeting Borrelia burgdorferi HtpG with a berserker molecule, a strategy for anti-microbial development.

Cell chemical biology·2023

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • Identifying homologous sequences is crucial for understanding protein evolution and function.
  • Current methods may struggle with limited or mixed peptide data from mass spectrometry or Edman sequencing.
  • Discovering novel protein and DNA sequences from unsequenced genomes remains a significant challenge.

Purpose of the Study:

  • To introduce two novel sequence similarity search algorithms, FASTS and FASTF.
  • To enable the identification of homologous sequences using multiple short peptide inputs.
  • To facilitate proteomic identification from organisms with unsequenced genomes.

Main Methods:

  • FASTS algorithm evaluates all possible arrangements of unordered peptides from mass spectrometry.

Related Experiment Videos

  • FASTF algorithm deconvolutes mixed peptide sequences using a greedy heuristic from Edman sequencing.
  • Both algorithms employ the FASTA comparison strategy and prioritize alignment probability over similarity score.

    • Main Results:

    • FASTS requires 15-20 residues in 3-4 peptides to identify homologous sequences with >=50% identity.
    • FASTF achieves equivalent sensitivity with ~25% more data than FASTS.
    • Statistical estimates showed accuracy within a factor of 10 for FASTS and 1000 for FASTF.
    • Both algorithms can identify homologues with divergences of 100-500 million years.

    Conclusions:

    • FASTS and FASTF offer efficient and sensitive methods for homologous sequence identification.
    • These algorithms significantly advance proteomic analysis for organisms with limited genomic data.
    • The developed tools expand the scope of comparative genomics and evolutionary studies.