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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...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Complementary DNA01:44

Complementary DNA

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Complementary DNA01:44

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Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

cisExpress: motif detection in DNA sequences.

Martin Triska1, David Grocutt, James Southern

  • 1Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, UK.

Bioinformatics (Oxford, England)
|June 25, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces cisExpress, a novel bioinformatics tool for detecting DNA sequence motifs in large genomic datasets. It identifies functional DNA elements by analyzing gene promoter similarities, enhancing genomic data analysis.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Analyzing genomic datasets and annotating DNA sequences is crucial for understanding gene function.
  • Identifying specific DNA sequence motifs is a key challenge in bioinformatics.
  • Existing methods may struggle with the scale of modern genomic and transcriptome data.

Purpose of the Study:

  • To present cisExpress, a novel genome-wide statistical approach for detecting DNA sequence motifs.
  • To provide a tool optimized for large-scale genomic datasets from public projects.
  • To enable more accurate functional annotation of DNA sequences.

Main Methods:

  • A genome-wide statistical approach analyzing promoter similarities of co-expressed genes.
  • Development of the cisExpress tool utilizing a task farming algorithm.
  • Leveraging shared memory nodes and computational cores for efficient processing.

Main Results:

  • Demonstration of the robust nature and validity of the cisExpress method.
  • Successful application to large-scale genomic and transcriptome datasets.
  • The tool is applicable across various species and genomic databases.

Conclusions:

  • cisExpress offers a powerful and efficient solution for DNA motif detection in large datasets.
  • The method enhances the extraction of functional information from genomic sequences.
  • This approach advances the field of bioinformatics and genomic data analysis.