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Arkadiy-Garber / MagicLamp

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
GNU General Public License v3.0
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Sources for HMMs for gene hits in LithoGenie #10

Closed rachelmugge closed 1 year ago

rachelmugge commented 2 years ago

Hi, I am trying to track down the source of HMMs for each gene hit within my dataset after running LithoGenie, and I was able to find most of them in the supplementary info for this paper: https://www.nature.com/articles/ncomms13219

However, I couldn't find sources for a handful of HMMs, listed here: lithogenie_hits_unknown_hmm_source.xlsx

I've searched the "hmms" folder on here also and while I found the hmm files, they did not list the accession number- where can I find this information?

Thank you!

Arkadiy-Garber commented 2 years ago

Hey! Those HMMs without accessions are custom-made specifically for this software. As in the HMMs from Anantharaman et al, my custom-made HMMs were compared against a reference database (nr) to calibrate an appropriate bit score cutoff for each.

rachelmugge commented 2 years ago

Ah okay, got it! So for the custom HMMs within MagicLamp (LithoGenie), I assume they were created using the same method as detailed in your FeGenie paper? (https://www.frontiersin.org/articles/10.3389/fmicb.2020.00037/full?ref=https://githubhelp.com#S9) Great methods section, by the way. Just wanting to give appropriate credit!

Arkadiy-Garber commented 2 years ago

Thanks, Rachel! I appreciate you sayin that.

Yes - any custom-made HMMs in MagicLamp were made using the same method as that described in the FeGenie paper. This method was actually first developed for AntiSMASH: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125804/.

seanmcallister commented 1 year ago

Seems like this can be closed?

rachelmugge commented 1 year ago

Yes, this info was helpful. Thank you!