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

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.

Sven Siebert1, Rolf Backofen

  • 1Department of Bioinformatics, Institute of Computer Science, Friedrich-Schiller-University Jena, Ernst-Abbe Platz 2, 07743 Jena, Germany.

Bioinformatics (Oxford, England)
|June 24, 2005
PubMed
Summary

This study introduces a novel RNA multiple alignment method (MARNA) that integrates primary and secondary structures. MARNA addresses challenges in combining pairwise alignments and generating missing structural data for improved RNA sequence analysis.

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

Enhanced IGFL1 translation in response to IL-1β is controlled by distinct 3'UTR elements.

PloS one·2026
Same author

Autoencoder/RandomForest-TabPFN for cross-cancer metabolomics: prostate and breast cancer diagnosis using paper spray and ion mobility-mass spectrometry techniques.

GigaScience·2026
Same author

A leader-repeat hairpin blocks extraneous CRISPR RNA production in diverse CRISPR-Cas13 systems.

The EMBO journal·2026
Same author

Comprehensive analysis of CRISPR array repeat mutations reveals subtype-specific patterns and links to spacer dynamics.

microLife·2026
Same author

The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.

microLife·2026
Same author

CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.

microLife·2026

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Functional RNA alignment necessitates incorporating secondary structure information.
  • Existing pairwise alignment methods use extended scores but face challenges in multiple alignment.
  • Key problems include combining pairwise alignments and handling sequences with missing structural data.

Purpose of the Study:

  • To present a novel approach for multiple RNA alignment (MARNA) considering both primary and secondary structures.
  • To develop a method that addresses the limitations of existing RNA alignment techniques.

Main Methods:

  • MARNA utilizes pairwise sequence-structure RNA comparisons to generate weighted alignment edges.
  • Weights signify sequential and structural conservation.

Related Experiment Videos

  • For sequences lacking explicit structures, low energy conformations are sampled to generate libraries.
  • The T-Coffee system, a consistency-based multiple alignment method, processes these libraries.

    • Main Results:

    • MARNA successfully integrates primary and secondary RNA structures for multiple alignment.
    • It generates weighted alignment edges reflecting conserved sequence and structure.
    • The method can infer secondary structures for sequences with missing data.
    • A consensus sequence and structure can be extracted from the generated multiple alignment.
    • MARNA demonstrated successful testing on datasets from the Rfam database.

    Conclusions:

    • MARNA offers a robust solution for multiple RNA sequence-structure alignment.
    • The approach effectively handles missing structural information, enhancing alignment accuracy.
    • MARNA provides a valuable tool for analyzing functional RNAs and their structures.