]> Protein pattern search (EMBOSS) protein:motifs http://bioweb.pasteur.fr/docs/EMBOSS/fuzzpro.html fuzzpro &emboss_init; input Input section sequence sequence -- protein [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 protein 8 seqsfile perl 1 required Required section pattern Search pattern (-pattern) perl " -pattern=$value" 2 The standard IUPAC one-letter codes for the amino acids are used. <BR> The symbol `x' is used for a position where any amino acid is accepted. <BR> Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr. <BR> Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met. <BR> Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzzpro). <BR> Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x. <BR> When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. <BR> A period ends the pattern. (Optional in fuzzpro). <BR> For example, [DE](2)HS{P}X(2)PX(2,4)C mismatch Number of mismatches (-mismatch) 0 perl " -mismatch=$value" 3 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 4 auto perl " -auto -stdout" 6