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Related Concept Videos

Protein Families02:47

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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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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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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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The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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muBLASTP: database-indexed protein sequence search on multicore CPUs.

Jing Zhang1, Sanchit Misra2, Hao Wang3

  • 1Department of Computer Science, Virginia Tech, 225 Stanger Street, Blacksburg, 24060, VA, USA. zjing14@vt.edu.

BMC Bioinformatics
|November 5, 2016
PubMed
Summary

A new protein sequence search tool, muBLASTP, uses database indexing for faster results than NCBI BLAST. It achieves significant speedups without compromising search sensitivity, making it ideal for modern multicore processors.

Keywords:
BLASTDatabase indexLocal alignmentMulticore

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics and Proteomics

Background:

  • The Basic Local Alignment Search Tool (BLAST) is crucial for sequence similarity searches in life sciences.
  • Current NCBI BLAST uses a query-indexed approach, which is sensitive but can be slow.
  • Existing database-indexed methods offer higher throughput but often lack the sensitivity of NCBI BLAST or are limited to nucleotide searches.

Purpose of the Study:

  • To develop a novel database-indexed BLAST algorithm for protein sequence search.
  • To achieve higher throughput comparable to other database-indexed methods while maintaining the sensitivity of NCBI BLAST.
  • To optimize the BLASTP algorithm for modern multicore processors.

Main Methods:

  • Developed a new index structure tailored for protein databases.
  • Re-factored the BLASTP algorithm to leverage database indexing.
  • Implemented optimizations for modern multicore CPU architectures.

Main Results:

  • The novel muBLASTP achieves identical search results to NCBI BLAST.
  • Single-threaded muBLASTP shows up to 1.75-fold end-to-end speedup over single-threaded NCBI BLAST.
  • Multi-threaded muBLASTP demonstrates up to 4.56-fold end-to-end speedup over multi-threaded NCBI BLAST on Intel Haswell CPUs.

Conclusions:

  • muBLASTP offers significantly improved throughput for protein sequence searches.
  • The new approach maintains the high sensitivity of NCBI BLAST.
  • The re-factored BLASTP algorithm is efficient on modern multicore processors with a manageable memory footprint.