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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.
RNA-seq03:21

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Sanger Sequencing01:57

Sanger Sequencing

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...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
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Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.

William Speier1, Michael F Ochs

  • 1Medical Imaging Informatics Group, University of California, Los Angeles, CA, USA. Speier@mii.ucla.edu

Bioinformatics (Oxford, England)
|September 5, 2012
PubMed
Summary

The BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) integration enables querying diverse biological annotation sources and standardizing data using the Distributed Annotation System (DAS) protocol for broader system compatibility.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Automated Sequence Annotation Pipeline (ASAP) and Distributed Annotation System (DAS) are key tools in bioinformatics.
  • BioDAS ProServer facilitates integration of diverse biological databases.

Purpose of the Study:

  • To develop an integrated interface between BioDAS ProServer and ASAP.
  • To standardize biological annotation data using the DAS protocol.
  • To enhance interoperability of annotation pipelines and databases.

Main Methods:

  • Integration of BioDAS ProServer with ASAP.
  • Utilizing the Distributed Annotation System (DAS) protocol for data standardization and querying.
  • Development of example implementations for specific biological data integration tasks.

Main Results:

  • A unified interface for querying diverse annotation sources.
  • Standardized output compatible with DAS-aware systems.
  • Successful integration examples including TRANSFAC, multi-platform array data, and UniProt.

Conclusions:

  • The BioDAS ProServer-ASAP integration facilitates flexible querying and standardization of biological annotation data.
  • This integration enhances the usability of annotation pipelines across different systems.
  • Example implementations demonstrate the practical application in gene set creation and data unification.