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Genome Annotation and Assembly

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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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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-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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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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UCSC Data Integrator and Variant Annotation Integrator.

Angie S Hinrichs1, Brian J Raney1, Matthew L Speir1

  • 1Genomics Institute, University of California, Santa Cruz, CA, USA.

Bioinformatics (Oxford, England)
|January 8, 2016
PubMed
Summary
This summary is machine-generated.

The UCSC Genome Browser now offers two new tools, the Data Integrator and Variant Annotation Integrator, for combining genomic datasets and annotating genetic variants with functional information.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Integrating and analyzing multiple genomic datasets is crucial for biological discovery.
  • Existing tools may lack flexibility in combining diverse data types or annotating genetic variants.
  • The UCSC Genome Browser is a widely used platform for genomic data visualization and analysis.

Purpose of the Study:

  • To introduce two novel web-based tools, the Data Integrator and Variant Annotation Integrator, designed to enhance genomic data analysis on the UCSC Genome Browser.
  • To provide users with improved capabilities for combining custom and public datasets, and for annotating genetic variants with functional predictions.

Main Methods:

  • Development of the Data Integrator to combine columns from multiple data tracks, displaying all items from a primary track with overlapping items from secondary tracks.
  • Implementation of the Variant Annotation Integrator for functional annotation of genetic variants, incorporating predictions of consequences for overlapping or nearby gene transcripts.
  • Integration of additional annotations such as dbNSFP scores, ENCODE regulatory data, and conservation scores into the Variant Annotation Integrator.

Main Results:

  • The Data Integrator facilitates the comprehensive integration of information from various genomic data sources.
  • The Variant Annotation Integrator provides enhanced functional annotations for genetic variants, including predicted effects on gene transcripts.
  • These tools support the inclusion of user-defined custom tracks and data from track hubs, increasing analytical flexibility.

Conclusions:

  • The new UCSC Genome Browser tools offer powerful and flexible solutions for integrating diverse genomic data and annotating genetic variants.
  • These advancements empower researchers to conduct more in-depth analyses of genomic information, aiding in the discovery of biological insights.
  • The tools are freely accessible, promoting wider adoption and advancement in the field of genomics research.