0.02 Prosite Pattern search K. Schuerer protein:motifs motifs prose prose perl "prose" 0 outfile "prose.out" infile Protein Sequence File perl " $value" 100 8 skip include abundant patterns perl ($value) ? " -s" : "" 3 0 report report occurences (-m) perl (defined $value && $value ne $vdef) ? " -m $value" : "" 3 short short shortest only (short) long longest only (long) all all subpatterns (all) With sequence ACErrrACErrrrDFGrrrDFG and pattern A-C-E-x(0,)-D-F-G shortest (default): reports only ACErrrrDFG longest: reports only ACErrrACErrrrDFGrrrDFG as match all: reports ACErrrACErrrrDFGrrrDFG, ACErrrACErrrrDFG, ACErrrrDFGrrrDFG and ACErrrrDFG case search case-sensitive perl ($value) ? " -c" : "" 3 0 warn warn of inproper prosite pattern syntaxe perl ($value) ? " -w" : "" 3 0 patterns User defined patterns 2 listfile Pattern List File (-l) perl ($value && !$pattern) ? " -l $value" : "" 1 File format : one pattern per line. This option exclude the Pattern option (-p).