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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses 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...
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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.
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Related Experiment Video

Updated: Jun 21, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Detecting species-site dependencies in large multiple sequence alignments.

Roland Schwarz1, Philipp N Seibel, Sven Rahmann

  • 1Institute of Hygiene and Microbiology, Josef-Schneider-Strasse 2/E1, 97080, Germany.

Nucleic Acids Research
|August 8, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a new method combining Fisher score embedding and correspondence analysis to uncover hidden patterns in multiple sequence alignments (MSAs). It reveals sequence-site interactions, crucial for understanding evolutionary signals and functional insights.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignments (MSAs) are vital for sequence analysis, yet existing methods struggle to reveal sequence-site interactions.
  • Site-specific methods (e.g., sequence logos) and sequence-based methods (e.g., clustering) fail to capture complex relationships within MSAs.

Purpose of the Study:

  • To develop a novel method for detecting and visualizing group-specific or conflicting signals within MSAs.
  • To bridge the gap in understanding informational elements at the sequence-site interaction level.

Main Methods:

  • Combines Fisher score-based embedding from profile hidden Markov models (pHMMs) with correspondence analysis.
  • Enables explorative investigation of alignments of various sizes manageable by pHMMs.

Main Results:

  • Successfully detects and visualizes group-specific and conflicting signals in MSAs.
  • Identifies sites of recombinatory horizontal gene transfer in Neisseria surface antigen LP2086.
  • Distinguishes between evolutionary and functional signals in the vitamin K epoxide reductase family.

Conclusions:

  • The proposed method offers a powerful approach for detailed analysis of MSAs, revealing insights into sequence-site interactions.
  • It enhances the understanding of evolutionary dynamics and functional mechanisms by uncovering hidden patterns in biological sequences.