0.1 motif arrangment search T. Junier, M. Pagni and P. Bucher T. Junier, M. Pagni and P. Bucher (2001), mmsearch: a motif arrangement language and search program, Bioinformatics 17:1234-1235. mmsearch mmsearch perl mmsearch 0 metamotif Metamotif perl " $value" motif 10 seqfile Sequence perl "$lt; $seqfile 11 in_format Ordinal number of each field in a line of input (-i) (defined $value && $value ne $vdef) ? " -i $value" : "" s1b2e3f4 1 Default format is 's1b2e3f4', which means: sequence (s) is field 1, begin of match (b) is field 2, end of match (e) is field 3 and feature (f) is field 4. The letters ca appear in any order, but must all be present. Somme frequently used formats have aliases, thes are 'pff' (the default) and 'gff'. search_opt Search options 2 overlap Allow matches to overlap (-O) perl (defined $value && $value != $vdef) ? " -O" : "" 0 all_feats Take into account all features (-X) perl (defined $value && $value != $vdef) ? " -X" : "" 0 If you have a protein which has domains A, B and A, in that order. By default, the protein will not match the metamotif 'A = A' because there are match data about B between the two A domains. Turn on this option make the protein matching the metamotif 'A = A'. output_opt Output options 3 out_format Output format (-o) perl (defined $value && $value ne $vdef) ? " -o $value" : "" nat nat: 'nativ' - string representation of the sequence pff pff: each match on a different line, no indivudal component motifs det det: 'detailed' - each component motif of each match spc spc: 'spacer' - show spacers (each per line) sep sep: 'hash marks' nat pff det spc sep all: report all formats nat pff det spc sep name Use this as metamotif name , only with 'pff' output (-n) perl (defined $value && $value ne $vdef) ? " -n $value" : "" perl $out_format =~ /pff/ METAMOTIF