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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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jul 13, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.

W C Ray1, R S Munson, C J Daniels

  • 1Children's Research Institute, The Ohio State University, 700 Childrens Dr., Columbus, OH 43205, USA. ray@biosci.ohio-state.edu

Bioinformatics (Oxford, England)
|December 26, 2001
PubMed
Summary

This study introduces tricross, a computational method for identifying conserved functional sequences across multiple genomes. The software successfully detected novel small RNA molecules and conserved promoter sequences missed by standard methods.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Standard gene-finding methods struggle with small proteins, regulatory elements, and functional RNAs due to size limitations, sequence variation, and lack of complete gene catalogs.
  • Conserved sequences across related organisms offer valuable information for identifying missed functional elements.
  • Existing tools like ORF-finders and pattern matchers have limitations in detecting all functional genomic sequences.

Purpose of the Study:

  • To develop and present a novel computational method, tricross, for detecting conserved functional sequences across multiple genomes.
  • To identify genes and other potentially functional sequences that may be missed by standard bioinformatics software.
  • To utilize conserved sequence information for enhanced genomic analysis.

Main Methods:

  • The tricross software performs multi-way cross-comparisons of sequence sets to identify conserved regions.
  • It generates graphical representations (VRML) and alignments of conserved sequence triples.
  • The method can be applied to both intergenic and gene sequences, and to pairs or triplets of genomes.

Main Results:

  • Tricross identified 101 intergenic sequences conserved among three Pyrococcus archaeal genomes.
  • Of these, 29 contained small RNA molecules, a recently discovered class in Archaea.
  • The remaining 72 sequences included conserved promoter elements and others of unknown significance.
  • The software also generated inter-genomic gene order dot-plots for various bacterial species.

Conclusions:

  • The tricross method effectively identifies conserved functional sequences, including small RNAs and promoters, that are often missed by conventional approaches.
  • This cross-genomic comparison strategy enhances the discovery of novel genomic elements.
  • Tricross is a versatile tool applicable to diverse genomic comparison tasks.