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gem-pasteur / macsyfinder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
GNU General Public License v3.0
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GA score threshold missing in some CasFinder profile [HELP] #72

Closed jpjarnoux closed 2 months ago

jpjarnoux commented 8 months ago

Hi, I'm trying to use the CasFinder profile. And HMMER/pyHMMER does not work on some of them. After a little searching, I noticed that for the listed below profile, there were no GA score thresholds. I would to know if that is expected and how it's managed to have sequenced annotated from 2 different scores.

cas10-like_IV-C_1 cas10-like_IV-C_2 cas10-like_IV-C_3 cas10-like_IV-C_4 cas11_IV-C_1 cas11_IV-C_2 cas11_IV-C_3 cas13x_VI-X_1 cas13y_VI-Y_1 cas6_IV-D_1 cas6_IV-D_2 cas6_IV-E_1 csf3-csf1_IV-E_1 csf4_IV-A1_1 csf4_IV-A1_2 csf4_IV-A_1 csf4_IV-E_1 gRAMP_III-E_1 recD_IV-D_1

CasFinder Models version 3.1.0

saphia commented 2 months ago

Hi Jérôme,

It is indeed possible for GA scores to be absent from HMM profiles if the authors of the profiles you are using did not compute them. MacSyFinder deals with profiles with or without these scores. It is described how [in the article of MacSyFinder version 2]() and in the documentation.

Best regards,

Sophie