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Profile scanning for three-dimensional structural patterns in protein sequences.

M Gribskov¹, M Homyak, J Edenfield

¹Molecular Biology Institute, University of California, Los Angeles 90024-1570.

Computer Applications in the Biosciences : CABIOS

|March 1, 1988

Summary

Profile analysis identifies structural motifs in protein sequences. This method uses position-specific scoring tables derived from probe sequences to rapidly scan target sequences for motif presence, enabling objective identification.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Profile analysis is a method for sequence similarity assessment.
It utilizes position-specific scoring tables (profiles) derived from aligned probe sequences.
These profiles are aligned with target sequences using dynamic programming.

Purpose of the Study:

To develop a library of profiles representing distinct structural motifs.
To enable rapid scanning of target sequences for the presence of these motifs.
To provide objective criteria for identifying structural motifs in proteins.

Main Methods:

Generating position-specific scoring tables (profiles) from aligned probe sequences.
Aligning target sequences against these profiles using dynamic programming.

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Establishing significance levels for profile-target comparisons.

Main Results:

A library of structural motif profiles is under development.
The method allows for rapid scanning of target sequences.
Objective determination of motif presence is facilitated by pre-set significance levels.

Conclusions:

The developed profile analysis approach enables efficient identification of structural motifs.
This method supports objective decision-making in protein structural analysis.
The profile library facilitates rapid motif discovery in biological sequences.