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Multi-species Conserved Sequences

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Related Experiment Video

Updated: Jun 17, 2026

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

A new measurement of sequence conservation.

Xiaohui Cai¹, Haiyan Hu, Xiaoman Li

¹Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Dr. MC0446, La Jolla, CA 92093, USA.

|December 24, 2009

Summary

A new sequence conservation measurement detects discontiguously conserved regions missed by current methods. This approach improves identification of functional genomic regions and aids in understanding sequence evolution.

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Sequence conservation analysis is crucial for understanding genome evolution and identifying functional regions.
Current methods often overlook functional regions with discontiguously conserved segments.
A novel measurement is needed to detect both contiguous and discontiguous conserved regions.

Purpose of the Study:

To define a new measurement for sequence conservation that accounts for both contiguous and discontiguous conserved segments.
To improve the detection of functional genomic regions that might be missed by existing methods.

Main Methods:

Proposed a novel sequence conservation measurement focusing on conserved segments within regions.
Defined conserved segments using the local alignment tool CHAOS.
Analyzed 1642 human functional non-coding regions and their mouse homologs.

Main Results:

Identified that current conservation analysis methods could miss at least 11% of functional regions.
Found that 72% of homologous regions identified by the new method were more similar to human sequences than those from UCSC.
The proposed method detected significantly more conserved segments compared to BLAST and discontiguous MegaBLAST.

Conclusions:

A new measurement based on conserved segments is critical for accurate sequence conservation analysis.
This method enhances the identification of local "orthologous" regions.
It offers new insights into discovering novel conserved functional regions in vertebrate genomes.