Published online 3 May 2016 | David Arndt1, Jason R. Grant1, Ana Marcu1, Tanvir Sajed1, Allison Pon1, Yongjie Liang1 and David S. Wishart1,2,3,*
PHASTER (PHAge Search Tool – Enhanced Release) is an upgraded version of the popular PHAST web server, designed for rapid identification and annotation of prophage sequences in bacterial genomes and plasmids. The new version is significantly faster, more efficient, and user-friendly compared to the original PHAST. Key improvements include:
1. **Software Optimizations**: Upgrading to BLAST+ (version 2.3.0+) and optimizing the computing cluster to handle more CPU cores (from 32 to 112), leading to a 4.3× speedup for typical bacterial genomes.
2. **Database Enhancements**: Reducing the size of the bacterial sequence database by removing redundant sequences and partitioning the database to improve search efficiency.
3. **User Interface Improvements**: Reimplementing the web interface using Ruby on Rails and modernizing the graphical genome viewer with JavaScript, making it faster, more robust, and visually appealing.
4. **Additional Features**: Implementing a 'quick query check' to handle pre-annotated genomes more efficiently and allowing users to save their searches using a cookie-based mechanism.
These enhancements make PHASTER capable of processing a typical bacterial genome in 3 minutes from raw sequence or 1.5 minutes with a pre-annotated GenBank file. The server is available at www.phaster.ca.PHASTER (PHAge Search Tool – Enhanced Release) is an upgraded version of the popular PHAST web server, designed for rapid identification and annotation of prophage sequences in bacterial genomes and plasmids. The new version is significantly faster, more efficient, and user-friendly compared to the original PHAST. Key improvements include:
1. **Software Optimizations**: Upgrading to BLAST+ (version 2.3.0+) and optimizing the computing cluster to handle more CPU cores (from 32 to 112), leading to a 4.3× speedup for typical bacterial genomes.
2. **Database Enhancements**: Reducing the size of the bacterial sequence database by removing redundant sequences and partitioning the database to improve search efficiency.
3. **User Interface Improvements**: Reimplementing the web interface using Ruby on Rails and modernizing the graphical genome viewer with JavaScript, making it faster, more robust, and visually appealing.
4. **Additional Features**: Implementing a 'quick query check' to handle pre-annotated genomes more efficiently and allowing users to save their searches using a cookie-based mechanism.
These enhancements make PHASTER capable of processing a typical bacterial genome in 3 minutes from raw sequence or 1.5 minutes with a pre-annotated GenBank file. The server is available at www.phaster.ca.