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

Computational analysis of RNAs.

S R Eddy1

  • 1Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63108, USA.

Cold Spring Harbor Symposia on Quantitative Biology
|March 27, 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

Noncoding RNA gene detection using comparative sequence analysis.

BMC bioinformatics·2002
Same author

Non-coding RNA genes and the modern RNA world.

Nature reviews. Genetics·2001
Same author

The distributed annotation system.

BMC bioinformatics·2001
Same author

A simple algorithm to infer gene duplication and speciation events on a gene tree.

Bioinformatics (Oxford, England)·2001
Same author

Computational identification of noncoding RNAs in E. coli by comparative genomics.

Current biology : CB·2001
Same author

Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.

Genome research·2001
Same journal

Functional and Mechanistic Interplay of Host and Viral Alternative Splicing Regulation during Influenza Infection.

Cold Spring Harbor symposia on quantitative biology·2020
Same journal

Myriad RNAs and RNA-Binding Proteins Control Cell Functions, Explain Diseases, and Guide New Therapies.

Cold Spring Harbor symposia on quantitative biology·2020
Same journal

Small RNA Function in Plants: From Chromatin to the Next Generation.

Cold Spring Harbor symposia on quantitative biology·2020
Same journal

U1 snRNP Telescripting Roles in Transcription and Its Mechanism.

Cold Spring Harbor symposia on quantitative biology·2020
Same journal

The THO Complex as a Paradigm for the Prevention of Cotranscriptional R-Loops.

Cold Spring Harbor symposia on quantitative biology·2020
Same journal

Biophysical Properties of HP1-Mediated Heterochromatin.

Cold Spring Harbor symposia on quantitative biology·2020
See all related articles

Stochastic context-free grammar (SCFG) algorithms analyze RNA secondary structure and sequence, aiding gene finding and homology searches. INFERNAL and RSEARCH programs identify distant RNA homologs by conserving both sequence and structure.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA sequence analysis is challenging due to conserved secondary structures.
  • Computational linguistics algorithms, specifically stochastic context-free grammars (SCFGs), are effective for RNA analysis.
  • SCFGs have enabled advancements in RNA gene-finding and homology search software.

Purpose of the Study:

  • To provide an accessible introduction to the strengths and weaknesses of SCFG methods.
  • To describe the current state of SCFG-based RNA similarity searching.
  • To highlight the capabilities of INFERNAL and RSEARCH programs.

Main Methods:

  • Utilizing stochastic context-free grammar (SCFG) algorithms for RNA analysis.
  • Applying SCFG methods to RNA gene-finding and homology searches.

Related Experiment Videos

  • Employing INFERNAL and RSEARCH programs for database searches.

    • Main Results:

    • SCFG algorithms offer robust methods for RNA secondary structure and sequence analysis.
    • SCFG-based approaches facilitate the identification of RNA genes and homologs.
    • INFERNAL and RSEARCH successfully identify distant RNA homologs by considering both sequence and structure conservation.

    Conclusions:

    • SCFG methods are powerful tools for RNA analysis, offering advantages in gene finding and homology detection.
    • The INFERNAL and RSEARCH programs represent the state of the art in SCFG-based RNA similarity searching.
    • Conserved RNA secondary structure is a critical feature for identifying homologous sequences.