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Related Concept Videos

Genomics02:02

Genomics

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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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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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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 residual plot is a statistical representation of data used to analyze correlation and regression results. It helps verify the requirements for drawing specific conclusions about correlation and regression. To obtain the residual plot, first, the residual for each data value is calculated, which is simply the vertical distance between the observed and the predicted value obtained from the regression equation.
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Related Experiment Video

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Rapid Analysis and Exploration of Fluorescence Microscopy Images
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Gepard: a rapid and sensitive tool for creating dotplots on genome scale.

Jan Krumsiek1, Roland Arnold, Thomas Rattei

  • 1Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Neuherberg, Germany. krumsiek@in.tum.de

Bioinformatics (Oxford, England)
|February 21, 2007
PubMed
Summary

Gepard software enables rapid dotplot creation using suffix arrays for efficiency. Its novel client-server mode allows online sequence analysis and functional annotation without data downloads.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Dotplots are essential for visualizing sequence similarity.
  • Existing software often requires extensive data downloads and setup.
  • There was a need for a more accessible and efficient dotplot generation tool.

Purpose of the Study:

  • To introduce Gepard, a user-friendly application for rapid dotplot creation.
  • To implement an efficient algorithm for dotplot calculation.
  • To develop a novel client-server mode for remote analysis.

Main Methods:

  • Utilized suffix arrays for optimizing dotplot calculation time complexity to Theta(m*log n).
  • Developed a client-server architecture for the application.
  • Integrated functional annotation for coloring dotplots.

Main Results:

  • Achieved significant reduction in dotplot calculation time.
  • Enabled on-the-fly sequence and annotation data processing.
  • Provided a user-friendly interface for interactive analysis.

Conclusions:

  • Gepard offers an efficient and accessible solution for generating and analyzing dotplots.
  • The client-server mode represents a novel advancement in sequence analysis software.
  • Facilitates quick visualization and functional interpretation of sequence data.