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Automated construction and graphical presentation of protein blocks from unaligned sequences
S Henikoff1, J G Henikoff, W J Alford
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA.
Gene
|October 3, 1995
Summary
Blockmaker is an automated system that identifies conserved protein sequence regions. It uses two algorithms for accuracy, aiding in database searches and PCR primer design.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- Protein families share conserved regions, often represented as ungapped blocks.
- Identifying these conserved blocks is crucial for understanding protein relationships and function.
Purpose of the Study:
- To introduce Blockmaker, an automated system for detecting conserved blocks in protein sequences.
- To provide biologists with a tool for analyzing protein sequence conservation.
Main Methods:
- Blockmaker utilizes two distinct algorithms: MOTIF and an automated Gibbs sampler.
- A 'reality check' approach validates blocks found by both methods.
- Sequence logos, incorporating sequence weights, visualize residue conservation.
Main Results:
- The system successfully identifies conserved protein blocks.
- Blocks generated by Blockmaker are effective for database searching and PCR primer design.
- Analysis of Caenorhabditis elegans Tc1 transposase homologs revealed previously unreported Tc1 homologs in fish and amphibians.
Conclusions:
- Blockmaker offers an efficient and reliable method for identifying conserved protein regions.
- The tool facilitates diverse applications in molecular biology research.
- Automated block identification enhances the discovery of novel sequence homologs across species.