Search a protein sequence with a motif emboss patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto Main sequence Motif to search for Output Report File Format DbMotif EMBL GENBANK GFF PIR SwissProt Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS Table TagSeq

You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html