]> Protein pattern search after translation (EMBOSS) nucleic:motifs protein:motifs http://bioweb.pasteur.fr/docs/EMBOSS/fuzztran.html fuzztran &emboss_init; input Input section sequence sequence -- dna [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 required Required section pattern Search pattern (-pattern) perl " -pattern=$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 gven 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 fuzztran) <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 fuzztran). <BR> For example, [DE](2)HS{P}X(2)PX(2,4)C mismatch Number of mismatches (-mismatch) 0 perl " -mismatch=$value" 3 advanced Advanced section frame Frame(s) to translate -- Translation frames (-frame) 1 1 2 2 3 3 F Forward three frames -1 -1 -2 -2 -3 -3 R Reverse three frames 6 All six frames 1 perl " -frame=$value" 4 table Code to use -- Genetic codes (-table) 0 Standard 1 Standard (with alternative initiation codons) 2 Vertebrate Mitochondrial 3 Yeast Mitochondrial 4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 Invertebrate Mitochondrial 6 Ciliate Macronuclear and Dasycladacean 9 Echinoderm Mitochondrial 10 Euplotid Nuclear 11 Bacterial 12 Alternative Yeast Nuclear 13 Ascidian Mitochondrial 14 Flatworm Mitochondrial 15 Blepharisma Macronuclear 16 Chlorophycean Mitochondrial 21 Trematode Mitochondrial 22 Scenedesmus obliquus 23 Thraustochytrium Mitochondrial 0 perl " -table=$value" 5 output Output section outfile outfile (-outfile) outfile.out perl " -outfile=$value" 6 auto perl " -auto -stdout" 8