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Related Experiment Video

Updated: May 11, 2026

In Situ Detection of Ribonucleoprotein Complex Assembly in the C. elegans Germline using Proximity Ligation Assay
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In Situ Detection of Ribonucleoprotein Complex Assembly in the C. elegans Germline using Proximity Ligation Assay

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Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans.

Daryanaz Dargahi1, David Baillie, Frederic Pio

  • 1Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada.

Plos One
|May 3, 2013
PubMed
Summary

Researchers identified 18 new Oligonucleotide-oligosaccharide binding (OB) fold genes in C. elegans using advanced bioinformatics. This improves genome annotation for divergent protein families and aids future gene discovery in model organisms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The C. elegans genome is well-annotated, but identifying novel genes, especially divergent protein families like the Oligonucleotide-oligosaccharide binding (OB) fold, is challenging.
  • The number of OB-fold proteins in C. elegans (n=46) is notably lower than in related eukaryotes like yeast (n=344) or fruit flies (n=84), suggesting potential underannotation.

Purpose of the Study:

  • To investigate the existence of unannotated OB-fold coding genes in the C. elegans genome.
  • To develop and apply a sensitive bioinformatics approach for identifying highly divergent protein families.

Main Methods:

  • Employed sensitive sequence-sequence, sequence-profile, and profile-profile similarity search methods.
  • Utilized 3D-structure prediction as a crucial filtering step to validate candidate sequences and minimize false positives.

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Published on: September 25, 2013

Related Experiment Videos

Last Updated: May 11, 2026

In Situ Detection of Ribonucleoprotein Complex Assembly in the C. elegans Germline using Proximity Ligation Assay
08:56

In Situ Detection of Ribonucleoprotein Complex Assembly in the C. elegans Germline using Proximity Ligation Assay

Published on: May 5, 2020

Automated Analysis of C. elegans Fluorescence Images using SegElegans
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Published on: October 10, 2025

Large-scale Gene Knockdown in C. elegans Using dsRNA Feeding Libraries to Generate Robust Loss-of-function Phenotypes
18:38

Large-scale Gene Knockdown in C. elegans Using dsRNA Feeding Libraries to Generate Robust Loss-of-function Phenotypes

Published on: September 25, 2013

Main Results:

  • Successfully predicted 18 novel coding genes containing the OB-fold in C. elegans.
  • These newly identified genes represent a significant expansion of the known OB-fold protein repertoire in this model organism.

Conclusions:

  • The study demonstrates that advanced bioinformatics strategies can improve the annotation of highly divergent protein families in C. elegans.
  • The developed approach is broadly applicable for large-scale genome analysis and can be adopted by consortia like WormBase for future genome releases.
  • This methodology holds general interest for annotating any genome and discovering novel genes across species.