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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
Genomics02:02

Genomics

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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RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
DNA Microarrays02:34

DNA Microarrays

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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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 Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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AnnoTrack--a tracking system for genome annotation.

Felix Kokocinski1, Jennifer Harrow, Tim Hubbard

  • 1Vertebrate Genome Analysis, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK. fsk@sanger.ac.uk

BMC Genomics
|October 7, 2010
PubMed
Summary
This summary is machine-generated.

The AnnoTrack software system aids large-scale genome annotation projects by integrating dispersed data and resolving conflicts. This tool supports collaborative efforts like the GENCODE project for accurate human genome reference annotation.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Growing demand for unified genome annotation tools in model organisms.
  • Collaborative genome annotation requires specialized software for data tracking and processing.
  • Expert-driven annotation relies on integrating evidence from diverse data sources.

Purpose of the Study:

  • To develop a software system (AnnoTrack) for large-scale genome annotation.
  • To support the GENCODE project's goal of accurate human genome reference annotation.
  • To facilitate efficient data integration and problem resolution in collaborative annotation.

Main Methods:

  • Development of the AnnoTrack software system.
  • Integration of data from multiple distributed sources.
  • Highlighting data conflicts and enabling problem prioritization and resolution.

Main Results:

  • AnnoTrack integrates dispersed data, identifies conflicts, and aids problem resolution.
  • The software supports the GENCODE project's aim for accurate human genome annotation.
  • AnnoTrack has been successfully used for over a year in large-scale genome annotation.

Conclusions:

  • AnnoTrack is a valuable tool for large-scale genome annotation.
  • The system is designed for easy setup and configuration with standard bioinformatics components.
  • AnnoTrack is available as open-source software for broader adoption.