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

Scoring hidden Markov models

C Barrett1, R Hughey, K Karplus

  • 1Department of Computer Engineering, University of California, Santa Cruz 95064, USA.

Computer Applications in the Biosciences : CABIOS
|April 1, 1997
PubMed
Summary
This summary is machine-generated.

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

Treatment-Related Adverse Events and Health-Related Quality of Life Associated With Immune Checkpoint Inhibitor Treatment for Mucosal Head and Neck Squamous Cell Carcinoma: A Scoping Review.

Head & neck·2026
Same author

Guidance for the gastrointestinal evaluation and management of iron deficiency in Sub-Saharan Africa.

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde·2024
Same author

Adult pure red cell aplasia at Universitas Academic Hospital, Bloemfontein, South Africa: A 9-year review.

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde·2022
Same author

Iatrogenic blood loss in critical care: A prospective observational study conducted at Universitas Academic Hospital in the Free State Province, South Africa.

The Southern African journal of critical care : the official journal of the Critical Care Society·2022
Same author

Haemophagocytic lymphohistiocytosis: Five years' experience at tertiary hospitals in Free State Province, South Africa.

The Southern African journal of critical care : the official journal of the Critical Care Society·2022
Same author

Epithelioid Angiomyolipoma - a case report and review of the literature.

Irish medical journal·2018
Same journal

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Computer applications in the biosciences : CABIOS·1998
Same journal

Two applications to facilitate the viewing of database search result files on the Macintosh.

Computer applications in the biosciences : CABIOS·1998
Same journal

BioWish: a molecular biology command extension to Tcl/Tk.

Computer applications in the biosciences : CABIOS·1998
Same journal

The Sequence Alerting Server--a new WEB server.

Computer applications in the biosciences : CABIOS·1998
Same journal

A software tool for the analysis of mass spectrometric disulfide mapping experiments.

Computer applications in the biosciences : CABIOS·1998
Same journal

SAMBA: hardware accelerator for biological sequence comparison.

Computer applications in the biosciences : CABIOS·1998
See all related articles

Choosing the right null model is crucial for accurate sequence comparison. A simple looping null model best identifies sequence matches using hidden Markov models (HMMs).

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Statistical Modeling

Background:

  • Statistical sequence comparison methods like hidden Markov models (HMMs) and generalized profiles assess sequence probability against a model.
  • Log-odds scoring evaluates this probability by comparing it to a null hypothesis, a simpler model representing general sequences.
  • Key questions arise regarding the optimal null model and the appropriate log-odds score threshold for defining a match.

Purpose of the Study:

  • To experimentally analyze the selection of null models and score thresholds in statistical sequence comparison.
  • To compare the performance of different null models and scoring methods within the Sequence Alignment and Modeling (SAM) software suite.

Main Methods:

  • Experimental analysis of various null models and score thresholds within the Sequence Alignment and Modeling (SAM) software suite.

Related Experiment Videos

  • Comparison of HMMer's log-odds scoring and SAM's Z-scoring method.
  • Evaluation of a simple looping null model based on the geometric mean of column probabilities in HMMs.

    • Main Results:

    • A simple looping null model demonstrated strong or superior performance across four discrimination experiments.
    • The chosen null model effectively balances sequence probability against a general sequence universe.
    • Log-odds scoring effectiveness was analyzed in conjunction with different null models and thresholds.

    Conclusions:

    • The simple looping null model is a highly effective choice for statistical sequence comparison using HMMs.
    • This finding optimizes the process of identifying sequence matches and improves the accuracy of bioinformatics analyses.
    • The study provides practical insights for selecting null models and thresholds in sequence analysis tools.