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

Automatic assessment of alignment quality.

Timo Lassmann1, Erik L L Sonnhammer

  • 1Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden. timo.lassmann@cgb.ki.se

Nucleic Acids Research
|December 20, 2005
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

Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer.

Scientific reports·2026
Same author

GeneSNAKE: a Python package for simulation of gene regulatory networks and perturbation-induced expression data.

Bioinformatics advances·2026
Same author

Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models.

Scientific reports·2026
Same author

AI succeeds in diagnosing rare diseases.

Nature·2026
Same author

A precision medicine approach to interpret a GATA4 genetic variant in a paediatric patient with congenital heart disease.

Human genomics·2026
Same author

The United Nations convention on rare diseases-A framework for research prioritization.

Frontiers in public health·2025
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

We developed a method to automatically assess genome alignment accuracy. This approach compares multiple alignments to ensure high quality for genomic annotation and data analysis pipelines.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Multiple sequence alignments are crucial for genomic annotation.
  • Automatic generation of high-quality alignments is computationally challenging.
  • Ensuring alignment accuracy is vital for downstream data analysis.

Purpose of the Study:

  • To develop an automated method for assessing the biological accuracy of multiple sequence alignments.
  • To introduce novel metrics for evaluating alignment quality.

Main Methods:

  • Comparing multiple alignments of the same sequences.
  • Introducing the average overlap score to identify difficult alignment cases.
  • Introducing the multiple overlap score to estimate biological correctness.

Related Experiment Videos

Main Results:

  • The MUMSA program implements the developed functions.
  • Demonstrated robustness and accuracy of the scoring functions on benchmark datasets.
  • The method effectively assesses biological accuracy of alignments.

Conclusions:

  • The new approach provides a simple and effective way to automatically evaluate alignment quality.
  • This tool enhances the reliability of genomic annotation pipelines by ensuring accurate input alignments.