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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Next-generation Sequencing03:00

Next-generation Sequencing

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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
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Multi-species Conserved Sequences

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Related Experiment Video

Updated: Jun 23, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Accelign: a GPU-based library for accelerating pairwise sequence alignment.

Felix Kallenborn1, Fawaz Dabbaghie2, Martin Steinegger2

  • 1Department of Computer Science, Johannes Gutenberg University, Mainz, 55099, Germany. kallenborn@uni-mainz.de.

BMC Bioinformatics
|June 21, 2026
PubMed
Summary
This summary is machine-generated.

Accelign offers accelerated pairwise sequence alignment on GPUs, significantly speeding up bioinformatics pipelines. This library enhances DNA, RNA, and protein sequence analysis, outperforming existing methods.

Keywords:
DNADynamic programmingGPUPairwise alignmentParallelizationProtein sequencesRNA

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Last Updated: Jun 23, 2026

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Increasing sequence data necessitates faster core algorithms.
  • Dynamic programming for pairwise sequence alignment is computationally intensive.
  • Efficient GPU implementations are crucial for bioinformatics pipelines.

Purpose of the Study:

  • To develop a library of accelerated pairwise sequence alignment algorithms for GPUs.
  • To address the quadratic time complexity of dynamic programming alignment.
  • To support various alignment types and sequence data.

Main Methods:

  • Developed Accelign, a library for CUDA-enabled GPUs.
  • Utilized a wavefront parallelization strategy adaptable to multiple dynamic programming algorithms.
  • Implemented local, global, and semi-global alignments for genomic and protein sequences.

Main Results:

  • Accelign achieves peak performance of 16.1 TCUPS and 9.1 TCUPS on a single GPU.
  • Demonstrated significant speedups over CPU-based and existing GPU-based libraries.
  • Showcased linear performance scaling with the number of GPUs.

Conclusions:

  • Accelign provides substantial speedups for pairwise alignment algorithms.
  • The library offers improved performance compared to prior implementations.
  • Accelign is publicly available for use and further development.