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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Related Experiment Video

Updated: Apr 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Fast and sensitive protein alignment using DIAMOND.

Benjamin Buchfink¹, Chao Xie², Daniel H Huson³

¹Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany.

|November 18, 2014

Summary

This summary is machine-generated.

We developed DIAMOND, a new open-source algorithm for faster sequence alignment. It significantly speeds up metagenomics and evolutionary analyses, offering 20,000x speedup over BLASTX with comparable sensitivity.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Sequence alignment is computationally intensive, posing a bottleneck in metagenomics and evolutionary studies.
Existing tools offer limited improvements in speed or sensitivity over BLASTX.

Purpose of the Study:

To introduce DIAMOND, an open-source algorithm for accelerated sequence alignment.
To address the computational challenges in analyzing large-scale sequencing data.

Main Methods:

Developed DIAMOND, an algorithm utilizing double indexing for efficient read alignment.
Compared DIAMOND's performance against established tools like BLASTX.

Main Results:

DIAMOND achieves up to 20,000 times greater speed than BLASTX on short sequencing reads.
The algorithm maintains a comparable level of sensitivity to existing methods.

Conclusions:

DIAMOND offers a significant advancement in sequence alignment speed for metagenomics and evolutionary research.
The open-source nature of DIAMOND promotes accessibility and further development in the field.