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Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

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Related Experiment Video

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Published on: September 28, 2017

Bcheck: a wrapper tool for detecting RNase P RNA genes.

Dilmurat Yusuf1, Manja Marz, Peter F Stadler

  • 1Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

BMC Genomics
|July 15, 2010
PubMed
Summary

Bcheck, a novel bioinformatics tool, efficiently identifies RNase P RNA genes in large-scale genomic data by combining pattern matching and covariance models. It accurately annotates microbial and eukaryotic genomes, discovering new genes and duplication events.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Industrial-scale genome annotation presents significant bioinformatics challenges.
  • Accurate identification of RNase P RNA genes is crucial for understanding cellular processes.
  • Existing methods may lack the speed or sensitivity required for large datasets.

Purpose of the Study:

  • To develop and present Bcheck, a robust bioinformatics tool for predicting RNase P RNA genes.
  • To combine pattern matching speed with covariance model sensitivity for enhanced gene detection.
  • To provide an efficient solution for large-scale genome annotation.

Main Methods:

  • Bcheck utilizes a library of subfamily-specific descriptor and covariance models.
  • It employs a two-step approach: fast filtering followed by sensitive gene modeling.
  • The tool integrates pattern matching for speed and covariance models for accuracy.

Main Results:

  • Bcheck identified RNase P RNA genes in 98% of 1024 microbial genomes within 4 hours.
  • It predicted 37 novel eukaryotic RNase P RNA genes, primarily in fungi.
  • Analysis of metagenomic data revealed 2909 unique RNase P RNA genes, many novel.

Conclusions:

  • Bcheck offers an efficient and accurate method for detecting RNase P RNA genes in large sequencing datasets.
  • The tool's combined approach of descriptor-based search and covariance modeling is highly effective.
  • Bcheck is available as a webserver and downloadable software for broad accessibility.