Hmmer Result - What Does Pp And Cs Mean?

Question

[backtofruits]

Hi, I have some hmmer results to analyze but I cannot find what the lines PP and CS mean? CS I cannot find in the documentation - what could this mean? PP stands for the per position posterior probability ?? So how possible it was - seen from the position before - that this protein occurs??? any idea/tipps/hints?

Alignments for each domain: == domain 1 score: 174.1 bits; conditional E-value: 3.3e-55 --HHHHHHHH-S--S-EEEES-SS--HHHHHHH--.STTTHHHHHHHH.H---HHHHHHH CS AXE1 186 GalalavaaleprvkkvvadyPfLsdfkRvvelalaeeaYdEitryfklldpkrereeev 245 Gal++a+aale+r+kk++ fLsd++Rv+++++ ++aY E+ ++f+l+dp++ re +v NODE_646 3 GALTVACAALEQRIKKAAQLCTFLSDYQRVWQIDQVKDAYLELREFFRLFDPRHSREFQV 62 9******************* PP Thanks for your help!

Answer 1

[robert.d.finn]

Hi,

PP, as you indicate is the posterior probability for an aligned residue. This represents the probability that this residue is assigned to the HMM state corresponding to this alignment column, as opposed to some other state. (Note that a residue can be confidently unaligned: a residue in an insert state or flanking N or C state may have high posterior probability.) The posterior probability is encoded as 11 possible characters 0-9*: 0.0≤p[HTML]

There is more detail in the HMMER documentation that is available at http://hmmer.janelia.org.

Hope this helps,

Rob

Answer 2

[backtofruits]

Thanks for your answer, Rob!

So say that in my calculated hmm the chance that an A occurs after an E is higher than that an S occurs, and so the A has a higher probability + gets a higher value?

CS is not explained, and also PP is not explained in more detail than this one line in the documentation...that's why I'm asking here :) Regards