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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The Stereotype Content Model (SCM) was first proposed by Susan Fiske and her colleagues (Fiske, Cuddy, Glick & Xu, 2002; see also Fiske, 2012 and Fiske, 2017). The SCM specifies that when someone encounters a new group, they will stereotype them based on two metrics: warmth—or that group’s perceived intent, and how likely they are to provide help or inflict harm—and competence—or their ability to carry out that objective. Depending on the warmth-competence...
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Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Novel Sequence Discovery by Subtractive Genomics
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PanDelos: a dictionary-based method for pan-genome content discovery.

Vincenzo Bonnici1, Rosalba Giugno2, Vincenzo Manca2

  • 1Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, Italy. vincenzo.bonnici@univr.it.

BMC Bioinformatics
|December 1, 2018
PubMed
Summary
This summary is machine-generated.

PanDelos is a new tool that efficiently discovers gene families across diverse genomes using information theory and network analysis. It outperforms existing methods in speed and accuracy for pan-genome analysis.

Keywords:
Distant genomesPan-genomek-mer dictionary

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Pan-genome analysis identifies gene family distribution across genomes.
  • Computational complexity and phylogenetic distance challenge homology detection.
  • Developing efficient similarity measures for pan-genome structures is crucial.

Purpose of the Study:

  • To present PanDelos, a novel tool for discovering pan-genome content in phylogenetically distant genomes.
  • To offer a parameter-free, fast, and accurate approach to homology relation discovery.

Main Methods:

  • Utilizes information theory and network analysis for homology discovery.
  • Employs k-mer multiplicity instead of sequence alignment for similarity measurement.
  • Integrates homology candidates into a network for community detection to extract gene groups.

Main Results:

  • PanDelos demonstrates superior performance compared to Roary and EDGAR.
  • Achieves faster running times and higher quality content discovery.
  • Validated on real and synthetic genomic datasets.

Conclusions:

  • PanDelos provides an effective solution for pan-genome analysis, especially for distant genomes.
  • The parameter-free, k-mer based approach offers significant advantages.
  • The software is publicly available for research use.