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Multi-species Conserved Sequences

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 Sites

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...

Conserved Binding Sites

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...

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 form...

Evolutionary Relationships through Genome Comparisons

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...

Conservation of Protein Domains

Conservation of Protein Domains

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 form...

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Related Experiment Video

Updated: Jun 17, 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

Algorithms for locating extremely conserved elements in multiple sequence alignments.

Huei-Hun E Tseng¹, Martin Tompa

¹Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA. lachesis@cs.washington.edu

BMC Bioinformatics

|December 22, 2009

Summary

This summary is machine-generated.

Researchers generalized ultraconserved elements to "Extremely Conserved Elements" across multiple species. An efficient algorithm identifies these elements when conserved across all species, aiding genomic research.

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Last Updated: Jun 17, 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

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

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

Published on: February 10, 2023

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Ultraconserved elements (UCEs) are genomic sequences conserved across human, mouse, and rat.
The discovery of UCEs in 2004 spurred significant research into conserved genomic regions.

Purpose of the Study:

To generalize the concept of UCEs to "Extremely Conserved Elements" (ECEs) conserved across arbitrary sets of species.
To develop and apply an efficient algorithm for identifying ECEs.

Main Methods:

Developed a linear-time algorithm to find ECEs conserved across all species in a multiple sequence alignment.
Demonstrated the NP-completeness of finding ECEs conserved across arbitrary subsets of species.
Applied the linear-time algorithm to a 44-vertebrate whole-genome alignment.

Main Results:

Catalogued 177 ECEs within the 44-vertebrate alignment using the efficient algorithm.
Showed that identifying ECEs conserved across arbitrary subsets of species is computationally complex (NP-complete).
Identified ECEs share characteristics with previously discovered UCEs.

Conclusions:

An efficient algorithm exists for identifying ECEs conserved across all or most aligned species, proving practical for research.
The computational difficulty of finding ECEs across arbitrary subsets highlights the complexity of evolutionary conservation patterns.
The identified ECEs provide valuable insights into conserved genomic regions and their evolutionary significance.