[Abstract] [NPS@ help] [Original server]

Paste a multiple protein alignment in clustalw format below : help

Weighting parameters (method of Sibbald and Argos) :
Number of shuffles per sequence to be performed (-N, int) :
Total weight (-W) :
Gap excision threshold (-X, fraction) :

Profile construction options :
Alignment boundaries :
If new alignment boundaries, keep sequences with at least residues in alignment region.
Score matrix :
Alignment mode :
Block profile mode (-b) :
The option -b is incompatible with options -a and -e !
Endgap weighting mode (-e) :
Gap weighting mode (-a and -s) : Symmetrically Asymmetrically
Circular profile (-c) :

Profile construction parameters :
Score matrix multiplier (-S, real) :
High cost initiation/termination score (-H, real) : // * = Low value
Low cost initiation/termination score (-L, real) :
Gap region threshold (-T, fraction) :
Gap excision threshold (-X, fraction) :
Gap opening penalty (-G, real) :
Gap extension penalty (-E, real) :
Gap penalty multiplier increment (-I, real) :
Maximum gap penalty multiplier (-M, real) :
Output score multiplier (-F, int) :

Scaling parameters (significance estimation procedure for profile match scores) :
Size of the random database (-N) :
Upper threshold of the probability range (-P) :
Lower threshold of the probability range (-Q) :