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Related Concept Videos

Protein Families02:47

Protein Families

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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...
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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...
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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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SWORD-a highly efficient protein database search.

Robert Vaser1, Dario Pavlović1, Mile Šikić2

  • 1Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia.

Bioinformatics (Oxford, England)
|September 3, 2016
PubMed
Summary

SWORD is a new protein database search tool that significantly outperforms BLAST in speed and sensitivity. This efficient implementation is ideal for large-scale bioinformatics analyses, offering guaranteed optimal alignments.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein database searching is crucial in bioinformatics.
  • Existing tools like BLAST face challenges with rapidly growing data volumes.
  • There's a need for faster and more sensitive search algorithms.

Purpose of the Study:

  • Introduce SWORD, an efficient protein database search tool.
  • Compare SWORD's performance against BLAST.
  • Highlight SWORD's suitability for large-scale database searches.

Main Methods:

  • Development of SWORD, an optimized protein database search implementation.
  • Benchmarking SWORD against BLAST across different sensitivity modes.
  • Evaluation of alignment sensitivity and optimality.

Main Results:

  • SWORD achieves 8-16x speed improvement over BLAST in sensitive mode.
  • SWORD is up to 68x faster than BLAST in fast, less accurate mode.
  • SWORD demonstrates superior sensitivity and guarantees optimal alignments for most datasets.

Conclusions:

  • SWORD offers a significant advancement in protein database search efficiency.
  • The tool is highly effective for large databases and demanding bioinformatics applications.
  • SWORD provides a compelling alternative to BLAST, enhancing research capabilities.