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Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences
1Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI 53141-2000, USA.
In Silico Biology
|August 23, 2006
Summary
Prophage Finder is a new PHP application that identifies prophage sequences in prokaryotic genomes. This tool aids in the accurate annotation of phage-related gene clusters within DNA sequences.
Area of Science:
- Genomics
- Bioinformatics
- Microbiology
Background:
- Prophage loci are frequently under-annotated in prokaryotic genome sequencing.
- Accurate identification of prophages is crucial for understanding prokaryotic-viral interactions.
Purpose of the Study:
- To develop and implement a computational tool for predicting prophage loci in prokaryotic genomes.
- To facilitate the rapid analysis and annotation of prophage sequences.
Main Methods:
- Developed a PHP application named Prophage Finder.
- Prophage Finder identifies prophages based on clusters of phage-related gene products.
- The application was benchmarked against manually curated prophage loci in annotated genomes.
Main Results:
- Prophage Finder successfully predicted prophage loci in benchmark genomic sequences.
- The tool provides detailed results to aid in prediction and analysis.
- Demonstrated the application's potential through analyses of draft prokaryotic genomes.
Conclusions:
- Prophage Finder is an effective tool for identifying prophage sequences.
- The application can improve the annotation accuracy of prokaryotic genomes.
- Available online, it offers a valuable resource for genomic research.
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