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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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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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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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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Variant Effect Prediction Analysis Using Resources Available at Gramene Database.

Sushma Naithani1, Matthew Geniza1,2, Pankaj Jaiswal3

  • 1Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA.

Methods in Molecular Biology (Clifton, N.J.)
|December 18, 2016
PubMed
Summary
This summary is machine-generated.

The Gramene database offers a phylogenetic framework for comparative plant genomics, providing access to annotated genomes, variation data, and gene expression resources. It empowers researchers to analyze their own genomic data using integrated tools and visualization platforms.

Keywords:
Ensembl plant genomesGenomic variationGenotype dataGrameneGramene Ensembl Genome BrowserIndelsNucleotide variationSNPVEPVariant effect predictor

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Comparative genomics enables understanding of plant evolution and function.
  • Access to curated genomic data and analysis tools is crucial for plant research.

Purpose of the Study:

  • To present the Gramene database (release #49) as a resource for plant comparative genomics.
  • To guide users in analyzing their genomic data using Gramene's features.

Main Methods:

  • Utilizing a phylogenetic framework and orthology-based projections.
  • Providing access to 39 complete and 6 partial plant genomes, variation data for 14 species, pathways for 58 species, and gene expression data for 14 species.
  • Facilitating data visualization and analysis via species-specific Genome Browsers and pathways.

Main Results:

  • Gramene release #49 offers comprehensive resources for comparative plant genomics.
  • Users can upload and visualize their genomic data, analyze nucleotide variation using the Variant Effect Predictor (VEP) tool, and process large datasets with command-line protocols.

Conclusions:

  • The Gramene database empowers the plant research community with integrated tools for comparative genomics.
  • Researchers can effectively analyze gene expression and variation data within a phylogenetic context.