Related Experiment Videos
Shotgun: getting more from sequence similarity searches.
1Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
Bioinformatics (Oxford, England)
|September 28, 1999
Summary
The Shotgun program enhances protein sequence analysis, identifying distant evolutionary relationships and superfamily members. This tool improves upon current methods for understanding protein structure-function.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Genomic sequencing reveals diverse protein structural classes.
- Understanding protein superfamilies is key to structure-function relationships.
- Current database searches struggle with distant sequence relationship detection.
Purpose of the Study:
- To develop a program to enhance sensitivity and utility of database search output.
- To improve the identification of distant sequence relationships.
Main Methods:
- Developed and utilized the Shotgun program.
- Employed BLAST database searches.
- Conducted control experiments to analyze false-positive rates.
Main Results:
- Identified new superfamily members and reconstructed known enzyme superfamilies.
- High Shotgun scores correlate with real evolutionary relationships.
- Demonstrated utility in identifying subgroup relationships and testing hypotheses.
Conclusions:
- The Shotgun program significantly improves the detection of distant protein sequence relationships.
- It aids in understanding protein evolution and family classification.
- Shotgun is a valuable tool for protein superfamily analysis.