Hi
I think the values of emission probabilities on MP states of a output pdf file does not match that of the .cm file.
In the attached cm file, the emission probabilities of state 30 is extracted as follows,
-3.167 -2.541 -3.627 1.624 -4.316 -2.747 0.395 -3.898 -3.644 3.055 -4.296 -0.329 0.071 -3.555 -1.803 -1.673
and the output pdf file is
It appears that CMV interprets the emission probs of the cm file as, from left to right, that of AA, AU, AG, AC, UU, ..., CU, CG.
However, In the infernal user's guide (p.102), the order of emission probabilities in a CM file is, from left to right, AA, AC, AG, AU, CA, CC, …, UG, UU.
I apologize if I have made a mistake, but I would appreciate it if you could check this. Thank you for your time.
RF00001.txt (please change .txt to .cm)
5S_rRNA.pdf
Hi
I think the values of emission probabilities on MP states of a output pdf file does not match that of the .cm file.
In the attached cm file, the emission probabilities of state 30 is extracted as follows,
-3.167 -2.541 -3.627 1.624 -4.316 -2.747 0.395 -3.898 -3.644 3.055 -4.296 -0.329 0.071 -3.555 -1.803 -1.673and the output pdf file is
It appears that CMV interprets the emission probs of the cm file as, from left to right, that of AA, AU, AG, AC, UU, ..., CU, CG.However, In the infernal user's guide (p.102), the order of emission probabilities in a CM file is, from left to right, AA, AC, AG, AU, CA, CC, …, UG, UU.
I apologize if I have made a mistake, but I would appreciate it if you could check this. Thank you for your time.
RF00001.txt (please change .txt to .cm)
5S_rRNA.pdf