]> Search a protein sequence with a motif (EMBOSS) protein:motifs http://bioweb.pasteur.fr/docs/EMBOSS/patmatdb.html patmatdb &emboss_init; input Input section sequence sequence -- Protein [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 protein 8 seqsfile perl 1 required Required section motif Protein motif to search for (-motif) perl " -motif=$value" 2 Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so 'AAA' matches 'aaa'. output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 3 auto perl " -auto -stdout" 5