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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

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Published on: July 12, 2022

LaTcOm: a web server for visualizing rare codon clusters in coding sequences.

Athina Theodosiou1, Vasilis J Promponas

  • 1Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.

Bioinformatics (Oxford, England)
|December 27, 2011
PubMed
Summary
This summary is machine-generated.

LaTcOm is a new web tool for identifying rare codon clusters (RCCs) using multiple algorithms. It offers user-friendly visualization and customizable parameters for sequence analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Rare codon clusters (RCCs) can impact protein translation efficiency.
  • Accurate identification of RCCs is crucial for understanding gene expression.
  • Existing methods for RCC detection may lack flexibility or comprehensive analysis.

Purpose of the Study:

  • To introduce LaTcOm, a novel web tool for rare codon cluster identification.
  • To provide multiple, user-selectable algorithms for RCC detection within a single interface.
  • To offer customizable parameters and visualization options for enhanced sequence analysis.

Main Methods:

  • Implementation of three RCC detection algorithms: %MinMax, a sliding window approach, and a modified linear-time algorithm.
  • Integration of user-tunable parameters, including codon-based scales (e.g., tRNA abundance, codon usage tables).
  • Inclusion of scale transformation options (linear, sigmoid) and flexible output formats (graphical, textual).

Main Results:

  • LaTcOm successfully integrates diverse RCC detection methodologies.
  • The tool provides a user-friendly graphical interface for sequence analysis.
  • Customizable parameters and visualization enhance the utility of RCC identification.

Conclusions:

  • LaTcOm offers a versatile platform for rare codon cluster analysis.
  • The tool facilitates deeper insights into codon usage and its impact on gene expression.
  • LaTcOm is a valuable resource for researchers in bioinformatics and genomics.