]> Creates matrices/profiles from multiple alignments (EMBOSS) nucleic:profiles protein:profiles http://bioweb.pasteur.fr/docs/EMBOSS/prophecy.html prophecy &emboss_init; input Input section sequence sequence -- gapany [set of sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 gapany 8 seqsfile perl 1 required Required section type Select type -- Profile type (-type) F Frequency G Gribskov H Henikoff F perl " -type=$value" 2 name Enter a name for the profile (-name) mymatrix perl " -name=$value" 3 advanced Advanced section profiletypesection Profile type specific options threshold Enter threshold reporting percentage (-threshold) acd @($(type)==F) 75 perl (defined $value && $value != $vdef)? " -threshold=$value" : "" 4 1 100 datafile Scoring matrix (-datafile) F G H acd @($(type)!=F) acd @($(type) = G: Epprofile H: EBLOSUM62 F: EBLOSUM62) perl ($value && $value ne $vdef)? " -datafile=$value" : "" 5 gapsection Gap options open Gap opening penalty (-open) perl $dogap acd $dogap 3.0 perl (defined $value && $value != $vdef)? " -open=$value" : "" 6 extension Gap extension penalty (-extension) perl $dogap acd $dogap 0.3 perl (defined $value && $value != $vdef)? " -extension=$value" : "" 7 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 8 auto perl " -auto -stdout" 9