High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Phage therapy utilizes bacteriophages to reduce bacterial populations.
• Phages introduce numerous bacterial and phage genes into ecosystems, impacting ecology.
• Understanding these genetic introductions is vital for predicting ecological consequences and ensuring phage therapy safety.

Purpose of the Study:

• To compare the effectiveness of manual and automated methods for annotating therapeutic phage genomes.
• To evaluate the accuracy and efficiency of SEA-PHAGE and Rime Bioinformatics protocols.
• To identify optimal strategies for high-quality phage genome annotation.

Main Methods:

• Twenty-seven phage genomes were annotated using both SEA-PHAGE and Rime Bioinformatics protocols.
• Structural annotation (gene calling) and functional annotation were performed and compared.
• SEA-PHAGE and Rime Bioinformatics' rTOOLS (v2) were the primary tools utilized.

Main Results:

• SEA-PHAGE identified more genes and start sites during structural annotation.
• However, Rime Bioinformatics' rTOOLS demonstrated superior performance in functional annotation, particularly for hypothetical proteins.
• Manual structural annotation was marginally superior, while automated functional annotation was more effective.

Conclusions:

• Automated functional annotation tools like rTOOLS offer a cost-effective and efficient alternative to manual methods.
• High-quality phage genome annotation is achievable with automated tools, supporting the advancement of phage therapy.
• This research facilitates safer and faster development of phage therapy by optimizing genome annotation processes.