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Quantitative computer analysis of signal sequence homologies in DNA
1International Genetic Engineering, Inc., Santa Monica, CA 90404.
Computer Applications in the Biosciences : CABIOS
|December 1, 1986
Summary
A new computer program identifies prokaryotic recognition sites, finding known signals and novel ones. It reveals that biological activity doesn't always correlate with strong sequence homology, requiring experimental validation.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genetics
Background:
- Prokaryotic gene regulation involves specific recognition sites for proteins like RNA polymerase, ribosomes, and cyclic-AMP receptor protein (CRP).
- Identifying these sites is crucial for understanding gene expression and regulation.
Purpose of the Study:
- To develop and apply a novel computational method for analyzing homologies to prokaryotic recognition sites.
- To investigate the relationship between sequence homology strength and biological activity of these sites.
Main Methods:
- Development of a computer program incorporating weighting factors to analyze consensus sequences.
- Application of the algorithm to known and potential prokaryotic recognition sites.
Main Results:
- The program successfully detected known signal sequence sites.
- Identified numerous novel sites with strong homology, but unknown biological function.
- Observed that some biologically active sites exhibit very weak homology.
Conclusions:
- Sequence homology strength is not a definitive predictor of biological function for recognition sites.
- Experimental validation is essential to determine the functional significance of identified homologies, especially those with weak sequence similarity.