prophecy is an EMBOSS program for creating a profile from a set of multiply aligned sequences. We'll use our OPS2_* alignment to show you prophecy
unix % prophecy
Creates matrices/profiles from multiple alignments
Input sequence: OPS2_.aln
Profile type
F : Frequency
G : Gribskov
H : Henikoff
Select type [F]: g
Enter a name for the profile [My matrix]: OPS2 sequences
Scoring matrix [Epprofile]:
Gap opening penalty [3.0]:
Gap extension penalty [0.3]:
Output file [outfile.prophecy]: OPS2_.prophecy