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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
RNA-seq03:21

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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...
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...
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.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Published on: July 12, 2022

Consistency of sequence-based gene clusters.

Roland Wittler1, Ján Maňuch, Murray Patterson

  • 1Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada. rwittler@techfak.uni-bielefeld.de

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|September 9, 2011
PubMed
Summary
This summary is machine-generated.

This study explores gene cluster consistency in comparative genomics. We present algorithms for simple models and prove NP-completeness for complex ones, advancing ancestral genome reconstruction.

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Computational biology

Background:

  • Gene order analysis is crucial for understanding functional and phylogenetic relationships between genomes.
  • Reconstructing ancestral gene clusters from contemporary species aids evolutionary studies.
  • The consistency criterion ensures that reconstructed gene clusters can coexist in a valid ancestral genome.

Purpose of the Study:

  • To investigate the computational complexity of the gene cluster consistency problem.
  • To develop efficient algorithms for verifying consistency in various gene cluster models.
  • To analyze consistency for gene cluster models with restricted gene multiplicities.

Main Methods:

  • Utilized combinatorial models to define gene clusters.
  • Applied algorithmic approaches to verify the consistency of reconstructed gene clusters.
  • Analyzed computational complexity, including linear-time algorithms and NP-completeness proofs.

Main Results:

  • Developed linear-time algorithms for verifying consistency in the model of adjacencies.
  • Established NP-completeness for more complex gene cluster models, such as common intervals.
  • Provided a comprehensive analysis of the consistency problem across different models and sequence types.

Conclusions:

  • The consistency of gene clusters is a fundamental problem in comparative genomics with varying computational difficulty.
  • Efficient solutions exist for simpler models, while complex models present significant computational challenges.
  • This research contributes to more accurate ancestral genome reconstruction and phylogenetic analysis.