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Yasas1994 / phage_contig_annotator

Annotates genes on putative phage contigs with protein orthologous groups using PHROGs
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Request for Database Updates and Custom Database Support in Phage Contig Annotator #3

Open ZihengWu opened 3 months ago

ZihengWu commented 3 months ago

Hello, Yasas! Thank you very much for developing the phage_contig_annotator and Jaeger software. They are fantastic and have been very helpful for my research. I noticed that phage_contig_annotator is based on the PHROGS database, which hasn't been updated since 2022. I was wondering if you have any plans to update the database for this great software? For example, switching to the frequently updated VOGDB database (https://www.vogdb.org). Additionally, are there any plans to update the software to allow users to annotate using their own databases?

Yasas1994 commented 3 months ago

Hi Ziehung,

Thanks for using Jaeger and phage_contig_annotator. I'm glad to hear that you find them useful :) I'm aware that PHROGS is long due for an update. My current plan is to replace it with a LLM, but this might take some time. I will add support for VOGDB and custom databases as soon as possible. Thanks for the great suggestion!

ZihengWu commented 3 months ago

Hello, Yasas, I am very pleased to receive your reply! There have indeed been studies showing that LLM can improve viral gene annotation. Your software is fantastic, especially the capability to visualize annotation results, which I greatly appreciate. I hope that with your continued efforts, they will become even better! Looking forward to your updates. :) Best regards.