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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.
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein function prediction and annotation in an integrated environment powered by web services (AFAWE).

Anika Jöcker1, Fabian Hoffmann, Andreas Groscurth

  • 1Plant Computational Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Bioinformatics (Oxford, England)
|August 14, 2008
PubMed
Summary

Automated gene annotation can be error-prone. AFAWE aids manual functional annotation by integrating diverse prediction tools and presenting results for easy comparison, improving accuracy and gene function discovery.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Automated gene annotation relies heavily on sequence similarity transfer.
  • This method can lead to incorrect annotations and missed functional insights.

Purpose of the Study:

  • To simplify and enhance the process of manual gene functional annotation.
  • To provide a user-friendly platform for comparing automated annotation results.

Main Methods:

  • Developed AFAWE (Automated Functional Annotation With Extended analysis) platform.
  • Integrated multiple automated gene function prediction tools as web services.
  • Implemented a comparative display of results with visual filters.
  • Enabled direct querying of primary databases for up-to-date information.
  • Provided an interface for adding manual annotations.

Main Results:

  • AFAWE facilitates the comparison of results from various automated annotation tools.
  • Visual filters aid in distinguishing reliable predictions from non-significant ones.
  • The platform ensures the use of current data by querying primary databases.
  • Users can add and share detailed manual annotations.

Conclusions:

  • AFAWE streamlines manual gene functional annotation, improving accuracy.
  • The tool enhances the discovery of gene functions, even when automated methods fail.
  • Extensible web service architecture allows for easy integration and updates.