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Updated: Jun 9, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Qualifying the relationship between sequence conservation and molecular function.

Gregory M Cooper¹, Christopher D Brown

¹Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. coopergm@u.washington.edu

Genome Research

|February 5, 2008

Summary

This summary is machine-generated.

Many genomic sequences have molecular function but lack evolutionary conservation. This occurs due to factors like phylogenetic scope, natural selection strength, and biological redundancy, suggesting some functionality may represent molecular noise.

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Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Sequence conservation is a key method for annotating genomic functional sequences.
Recent studies reveal numerous metazoan genomic sites with molecular function but no detectable conservation across species.

Purpose of the Study:

To explore explanations and implications for functional sequences lacking evolutionary conservation.
To discuss the interplay between phylogenetic scope, natural selection, and sequence turnover in metazoan genomes.

Main Methods:

Comparative genomics analysis.
Phylogenetic comparative methods.
Theoretical modeling of evolutionary constraints.

Main Results:

Phylogenetic scope impacts the detection of sequence conservation and function; distant species comparisons offer high specificity but lower sensitivity.
Functional sequences under weak natural selection, or those that are degenerate/redundant, are prone to turnover, especially in highly divergent species.
Many nonconserved sequences likely possess biochemical functions that are not under evolutionary constraint, representing molecular noise.

Conclusions:

The presence of nonconserved functional sequences does not necessarily imply widespread functional importance in vertebrate genomes.
A significant portion of observed "functionality" may represent molecular noise with minimal phenotypic impact.