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

Intermediate sequences increase the detection of homology between sequences

J Park1, S A Teichmann, T Hubbard

  • 1Cambridge Centre for Protein Engineering, UK.

Journal of Molecular Biology
|November 21, 1997
PubMed
Summary

Identifying evolutionary relationships between distantly related protein sequences can be challenging. This study introduces an intermediate sequence method, enhancing the detection of these distant protein sequence relationships by 70%.

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

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Nature·2002
Same author

Small-molecule metabolism: an enzyme mosaic.

Trends in biotechnology·2001
Same author

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.

Journal of molecular biology·2001
Same author

Identification of a vibrational frequency corresponding to H-atom translocation in hypericin.

Photochemistry and photobiology·2001
Same author

Tumor cell toxicity of hypericin and related analogs.

Photochemistry and photobiology·2001
Same author

Self-assembled monolayer of a redox-active calix[4]arene: voltammetric recognition of the Ba2+ ion in aqueous media.

Analytical chemistry·2001

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Homologous sequences diverging beyond direct comparison pose challenges in evolutionary relationship detection.
  • Existing methods struggle to identify distant evolutionary links between protein sequences.

Purpose of the Study:

  • To evaluate the effectiveness of using intermediate sequences to identify distantly related protein evolutionary relationships.
  • To improve the detection rate of evolutionary relationships in protein sequence databases.

Main Methods:

  • Utilized the PDB40D database containing 971 protein domains with <= 40% residue identity.
  • Performed all-against-all comparisons using FASTA to identify direct matches.
  • Employed an intermediate sequence strategy by searching PDB40D sequences against the OWL database.

Related Experiment Videos

Main Results:

  • Direct FASTA comparison detected only 15% (320/2143) of known evolutionary relationships with a 1% false positive rate.
  • The intermediate sequence approach identified 550 evolutionary relationships with a 1% false positive rate.
  • This method increased the detection of evolutionary relationships by 70%.

Conclusions:

  • Intermediate sequences significantly enhance the identification of distant protein evolutionary relationships.
  • The developed method offers a more sensitive approach for evolutionary analysis in large protein sequence datasets.
  • This strategy improves upon direct comparison methods for uncovering hidden evolutionary connections.