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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.
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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Evolutionary Relationships through Genome Comparisons

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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.
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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...
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Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is formed in...

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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

Andrew M Waterhouse1, James B Procter, David M A Martin

  • 1School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Bioinformatics (Oxford, England)
|January 20, 2009
PubMed
Summary
This summary is machine-generated.

Jalview Version 2 offers interactive editing, analysis, and annotation for multiple sequence alignments. This powerful tool is available as a web applet and a desktop application, enhancing bioinformatics workflows.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Jalview 2 is a freely available software system for analyzing biological sequences.
  • It provides interactive editing, analysis, and annotation of multiple sequence alignments.
  • The software is accessible via a Java applet for web applications and a desktop application.

Purpose of the Study:

  • To introduce Jalview Version 2, a comprehensive system for multiple sequence alignment management.
  • To highlight its interactive features, analysis capabilities, and annotation tools.
  • To detail its availability as both a web-based applet and a standalone desktop application.

Main Methods:

  • Interactive WYSIWYG editing of multiple sequence alignments.
  • Utilizes web services for advanced analysis, including sequence alignment and secondary structure prediction.
  • Integrates with public databases and DAS servers for data retrieval.

Main Results:

  • Jalview 2 provides a user-friendly interface for sequence alignment editing and visualization.
  • Offers linked structure display with Jmol for integrated analysis.
  • Facilitates retrieval of diverse biological data from various sources.

Conclusions:

  • Jalview 2 enhances bioinformatics research through its versatile alignment editing and analysis features.
  • The dual availability as an applet and desktop application increases accessibility for researchers.
  • It serves as a valuable tool for the interpretation of biological sequence data.