Table 1 Phamerator Features and Modifications
From: Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies
Feature | Updates provided in new version | Justification |
|---|---|---|
Biopython compatibility | Works with BioPython 1.64 | Continued compatibility with future Biopython versions |
Building the Phamerator database | Added prompts for username, password, server location, and database name at each step | The new prompts replace what was once written directly into the code |
ClustalO alignments | ClustalO may be used instead of ClustalW to perform alignments | ClustalO is newer and is faster |
Computation progress | Fixed script displaying the progress of BLAST and ClustalW | Helps users estimate when these jobs will finish |
Pham and cluster tables | Column listing conserved domains for each pham was added to these tables | Used to quickly determine putative functions of proteins in a pham |
Domain and pham labels in genome maps | Added whitespace to the right of these maps | Labels near the end of these maps are now visible |
Delete BLAST and ClustalW scores | Users are prompted to delete or keep all scores when adding or removing phages | Scores can be deleted following major modifications to the database |