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

HMM-Kalign: a tool for generating sub-optimal HMM alignments.

Emmanuelle Becker1, Aurélie Cotillard, Vincent Meyer

  • 1CEA, iBiTecS, URA 2096, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif sur Yvette, F-91191 France.

Bioinformatics (Oxford, England)
|October 9, 2007
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

Deciphering protein mutation-phenotype linkages from CRISPR-based tiling mutagenesis screens.

Cell systems·2026
Same author

clickBrick prompt engineering: optimizing large language model performance in clinical psychiatry.

Npj mental health research·2026
Same author

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens.

bioRxiv : the preprint server for biology·2026
Same author

Optimized Quantitative Bacterial Two-Hybrid (qB2H) for Protein-Protein Interaction Assessment.

Computational and structural biotechnology journal·2026
Same author

Heterozygous loss-of-function alleles associate the conserved 3'-5' exoribonuclease EXOSC10 with hypersensitivity to the anticancer drug 5-fluorouracil.

Molecular oncology·2026
Same author

Unveiling a missing component of the atypical type IV secretion system required for natural transformation of <i>Helicobacter pylori</i>.

bioRxiv : the preprint server for biology·2026

A new tool, hmmkalign, uses a generalized Viterbi algorithm to improve protein sequence alignment for remote homology detection. This enhances comparative modeling by generating optimal and sub-optimal alignments between sequences and Hidden Markov Models.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple sequence alignments (MSA) and profiles aid in detecting remote protein homologies.
  • This increases the utility of comparative modeling for protein structure prediction.
  • Accurate alignment of highly divergent homologous proteins remains a challenge.

Purpose of the Study:

  • To present a novel computational tool for generating optimal and sub-optimal sequence alignments.
  • To address the challenge of aligning highly divergent homologous proteins.

Main Methods:

  • Development of a tool based on a generalized Viterbi algorithm.
  • Implementation as a new function, hmmkalign, within the HMMER package.
  • The algorithm generates alignments between a protein sequence and a Hidden Markov Model (HMM).

Related Experiment Videos

Main Results:

  • The hmmkalign function provides a method for generating optimal and sub-optimal alignments.
  • This tool facilitates more accurate remote homology detection.
  • Improved alignments can enhance the accuracy of comparative modeling.

Conclusions:

  • The generalized Viterbi algorithm implemented in hmmkalign offers an effective solution for aligning divergent homologous proteins.
  • This advancement supports more reliable protein structure prediction through comparative modeling.