I am using Megan CE version 6.21.1 with long read metagenomic sequences to analyze the functional composition of the metagenome. I am finding that many InterPro annotations are incorrect. I have included one example here. Megan assigned WP_148073251.1 as IPR039808 cadherin. When I use the protein sequence to perform an InterPro scan, it does not match to cadherin. The read aligns quite well with the protein ID WP_148073251.1; however, the assigned InterPro identifier seems incorrect. I have attached the screenshot below. Please suggest.
Hi, I just wanted to follow up and inquire about any suggestions regarding the interpro annotation mentioned earlier. It occurred with multiple annotations. Please let me know if you require additional information.
Hi @Pgautam,
Apologies for missing this earlier. We have discontinued providing InterPro annotations in MEGAN7. Since you’re using MEGAN6 with the last mapping file from 2022, one possibility is that the mappings have been updated since then, or it could be a bug. I recommend transitioning to MEGAN7 and using other functional annotation sources. SEED is quite up-to-date, and while there has been discussion about supporting InterPro, I can’t guarantee when or if that will happen.
Feel free to send us your output file, and I’ll take a look and update you.
Best regards,
Anupam
Thank you for letting me know. I will try Megan 7 with a new mapping file and functional annotation from SEED. Also, do you know if Megan 7 will be available as a bioconda package soon?
Updating MEGAN7 on Conda will take some time. However, if you need to install it on a specific operating system, feel free to reach out. MEGAN can also be installed without the GUI (for use on clusters, etc.). Let me know if you’d like the installation commands!
Best regards,
Anupam
Hi Anupam,
Yes, could you please send me the installation commands? I am using a cluster environment, so I can’t use the GUI version.
Thank you,
Pratima
pgautam1@umbc.edu
Hi @Pgautam,
I’ve sent an email to the provided address with the MEGAN7 installation instructions for the cluster. Let me know if you have any further questions.
Best regards,
Anupam
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