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Related Concept Videos

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...
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Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Genomics02:02

Genomics

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...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Updated: Jul 5, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

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Published on: December 22, 2017

Efficient evidence-based genome annotation with EviAnn.

Aleksey V Zimin1,2, Daniela Puiu3,4, Mihaela Pertea3,4

  • 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. alekseyz@jhu.edu.

Nature Methods
|July 3, 2026
PubMed
Summary
This summary is machine-generated.

EviAnn, an evidence-based gene annotation system, leverages abundant transcript and protein data for accurate eukaryotic genome annotation. It outperforms existing tools, offering faster and more efficient gene finding.

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Published on: May 28, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Traditional ab initio gene finders were limited by scarce gene expression data.
  • Modern sequencing provides abundant transcript and protein evidence for genome annotation.
  • Existing tools underutilize this wealth of evidence.

Purpose of the Study:

  • To develop EviAnn (Evidence-based Annotator), a novel eukaryotic gene annotation system.
  • To create a data-driven approach that prioritizes transcript and protein evidence over ab initio predictions.
  • To improve the efficiency and accuracy of eukaryotic genome annotation.

Main Methods:

  • EviAnn builds exon-intron structures directly from transcript alignments and protein homology.
  • It employs a data-driven strategy, contrasting with traditional ab initio methods.
  • The system was evaluated against leading annotation packages like BRAKER3, MAKER2, and FINDER.

Main Results:

  • EviAnn consistently outperforms BRAKER3, MAKER2, and FINDER in gene annotation accuracy.
  • The system utilizes significantly less computational time compared to existing tools.
  • A mammalian genome can be annotated in under an hour on a single multicore server.

Conclusions:

  • EviAnn represents a significant advancement in evidence-based eukaryotic gene annotation.
  • The system efficiently utilizes abundant transcriptomic and proteomic data for improved accuracy.
  • EviAnn offers a faster, more resource-efficient alternative for genome annotation tasks.