I am a first timer in phosphorylation motif analysis:

Motif-X website has been down for over a year now, the alternative way is to use the r-motifx. Still, motif-x looks like the most widely used search algorithm for the phosphorylation motif search. Furthermore, the Motif-All algorithm in the Phsohositeplus website is also a widely used resource.

My question is, r-motifx and motif-all provide a different number (count in foreground match) of "motifs" from the same background and foreground files, how should I make a better decision form both outputs?

Just an example from my dataset I posted below:

#Motif_all_output

Motif ; Count in Foreground; Count; in Background; Z-score; P; Value

___R__[pS]______; 79; 48181; 12.88284991; 0

______[pS]P_____ 124; ;46556 20.66575415; 0

_S____[pS]P_____ 21; 5595; 10.33583456; 0

_L_R__[pS]______ 24; 5287; 11.9355553; 0

__S___[pS]P_____ 17; 6229; 8.030534286; 0

____P_[pS]P_____ 22; 3779; 12.56102052; 0

______[pS]P_S___ 26; 5687; 12.44697543; 0

______[pS]P__S__ 24; 6109; 11.2534285; 0

______[pS]P___S_ 23; 5453; 11.34949135; 0

______[pS]P___K_ 17; 2640; 11.47146789; 0

#R-Motif-X output

motif; score; fg.matches; fg.size; bg.matches; bg.size; fold.increase

......SP..... ; 307.6527 ; 111; 286; 36291; 683652; 7.311275

.L.R..S......; 314.1722; 22; 175; 3953; 647361; 20.587535

...R..S......; 307.6527; 39 ; 153; 31520; 643408; 5.203235

Here, in the ---sP---- motif the foreground count (111) (r-motifx) or count in foreground (124) (MotifAll) has different output.