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

ConStruct: Improved construction of RNA consensus structures.

Andreas Wilm1, Kornelia Linnenbrink, Gerhard Steger

  • 1Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Universitätsstr, 1, D-40225 Düsseldorf, Germany. wilm@biophys.uni-duesseldorf.de

BMC Bioinformatics
|April 30, 2008
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

Sustainable data analysis with Snakemake.

F1000Research·2025
Same author

Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses.

Frontiers in oncology·2025
Same author

PIPLOM: prediction of exogenous peptide loading on major histocompatibility complex class I molecules.

Bioinformatics advances·2025
Same author

Viroids, Satellite RNAs and Prions: Folding of Nucleic Acids and Misfolding of Proteins.

Viruses·2024
Same author

In-depth analysis of human virus-specific CD8<sup>+</sup> T cells delineates unique phenotypic signatures for T cell specificity prediction.

Cell reports·2023
Same author

"Pathomorphogenic" Changes Caused by Citrus Bark Cracking Viroid and Transcription Factor TFIIIA-7ZF Variants Support Viroid Propagation in Tobacco.

International journal of molecular sciences·2023
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Aligning non-coding RNAs (ncRNAs) is challenging. CONSTRUCT is a graphical tool that aids in correcting ncRNA alignments using sequence, thermodynamics, and covariation, improving structure prediction.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Accurate alignment of homologous non-coding RNAs (ncRNAs) is crucial for downstream analyses like structure prediction and phylogenetic inference.
  • Existing automated ncRNA alignment methods often require manual correction, which is time-consuming and prone to errors.
  • Mathematical complexity and imperfect scoring functions contribute to the difficulty in achieving high-quality ncRNA alignments.

Purpose of the Study:

  • To present an extended version of CONSTRUCT, a semi-automatic graphical tool for creating accurate RNA sequence and structure alignments.
  • To enhance the process of ncRNA alignment correction by integrating sequence, thermodynamic data, and covariation measures.
  • To provide a user-guided approach for refining ncRNA alignments, facilitating improved secondary and tertiary structure predictions.

Related Experiment Videos

Main Methods:

  • CONSTRUCT integrates sequence alignment algorithms with thermodynamic data and covariation analysis.
  • A consensus dotplot guides users by displaying optimal base pairs and covariation information during alignment correction.
  • The tool facilitates prediction of optimal and suboptimal secondary structures, as well as tertiary interactions, post-alignment refinement.

Main Results:

  • CONSTRUCT effectively guides users in correcting initial ncRNA alignments.
  • The tool demonstrates successful secondary consensus structure prediction for challenging SECIS elements.
  • CONSTRUCT enables prediction of tertiary interactions in viral internal ribosome entry site sequences and optimization of benchmark alignments with low sequence identity.

Conclusions:

  • CONSTRUCT's graphical interface simplifies alignment correction by incorporating structural constraints.
  • The software combines multiple algorithms for predicting both secondary and tertiary RNA structures.
  • CONSTRUCT is available for download, offering a valuable resource for RNA alignment and structure prediction.