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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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What is Variation?01:14

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Apart from the measures of central tendency, distribution, outliers, and the changing characteristics of data with time, an important characteristic of any data set is its variation or spread. In some data sets, the data values are concentrated closely near the mean; in others, the data values are more widely spread out from the mean.
The range, standard deviation, standard error, and variance are the different measures of variation.
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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Genome Size and the Evolution of New Genes03:21

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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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When an archer pulls the string in a bow, he saves the work done in the form of elastic potential energy. When he releases the string, the potential energy is released as kinetic energy of the arrow. A capacitor works on the same principle in which the work done is saved as electric potential energy. The potential energy (UC) could be calculated by measuring the work done (W) to charge the capacitor.
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Variation01:19

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An important characteristic of any set of data is the variation in the data. In some data sets, the data values are concentrated closely near the mean; in other data sets, the data values are more widely spread out from the mean. The most common measure of variation, or spread, is the standard deviation, which is the square root of variance.
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Seave: a comprehensive web platform for storing and interrogating human genomic variation.

Velimir Gayevskiy1, Tony Roscioli2,3,4, Marcel E Dinger1,5,6

  • 1Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.

Bioinformatics (Oxford, England)
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Summary

Seave is a new web platform for storing, annotating, and filtering genetic variants, including structural variants. It simplifies the interpretation of human genetic variation by integrating diverse data sources and prediction algorithms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Human genetic variation studies are crucial but hampered by variant interpretation challenges.
  • Interpreting variants, especially structural variants, requires integrating data from multiple sources and in silico predictions.

Purpose of the Study:

  • To introduce Seave, an intuitive web platform for secure storage, annotation, and filtering of genetic variants.
  • To address the bottleneck in variant interpretation by providing a unified solution for diverse variant types.

Main Methods:

  • Developed Seave, a web platform supporting secure storage and querying of all variant types, including structural and copy number variants.
  • Integrated allele frequencies, pathogenicity assessments from popular databases, and in silico prediction scores.
  • Enabled filtering by inheritance patterns (including somatic), quality, allele frequencies, and curated gene lists.

Main Results:

  • Seave facilitates comprehensive annotation and filtering of genetic variants.
  • The platform efficiently handles whole genome data and diverse variant types.
  • Seave streamlines the process of variant interpretation for researchers.

Conclusions:

  • Seave provides a robust and user-friendly solution for managing and interpreting genetic variants.
  • The platform enhances the study of human genetic variation by overcoming interpretation bottlenecks.
  • Seave is available via a public demo, with source code and deployment options provided.