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Genome Annotation and Assembly03:36

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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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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.
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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 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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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

Jon Duvick1, Daniel S Standage2, Nirav Merchant3

  • 1Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011.

The Plant Cell
|March 30, 2016
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Summary
This summary is machine-generated.

The xGDBvm software streamlines genome annotation by integrating analysis tools into a virtual machine, making complex gene structure prediction scalable for researchers. This bioinformatics solution simplifies data management and analysis for diverse genomic applications.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Genome-wide gene structure annotation involves complex computational steps.
  • Current collaborative annotation methods are not scalable with rapid sequence generation.
  • There is a need for efficient, accessible tools for genome annotation.

Purpose of the Study:

  • To develop a scalable software solution for genome annotation.
  • To provide an intuitive platform for accessing gene structure analysis tools.
  • To facilitate efficient de novo annotation, reannotation, and comparative genomics.

Main Methods:

  • Developed xGDBvm, a virtual machine with preconfigured genome analysis tools.
  • Utilized a unified web interface for managing inputs, parameters, and HPC resources.
  • Integrated spliced alignment, gene structure prediction, and genome browser display.
  • Included yrGATE for reannotation of problematic gene predictions.

Main Results:

  • xGDBvm simplifies genome annotation through a graphical user interface and automated workflows.
  • The software supports local or remote high-performance computing (HPC) for analysis.
  • Outputs are displayed in a genome browser with tools for editing and quality assessment.
  • Facilitates annotation of multiple genomes, data archiving, and sharing.

Conclusions:

  • xGDBvm offers a scalable and accessible solution for genome annotation challenges.
  • The platform supports various use cases, including training and teaching.
  • Enhances the efficiency and reproducibility of gene structure annotation in bioinformatics research.