appl: fuzztran [
  documentation: "Protein pattern search after translation"
  groups: "Nucleic:Motifs, Protein:Motifs"
]

section: input [ info: "input Section" type: page ]
seqall: sequence  [
  parameter: "Y"
  type: "dna"
]

endsection: input

section: required [ info: "required Section" type: page ]
string: pattern  [
  required: "Y"
  prompt: "Search pattern"
  help: "The standard IUPAC one-letter codes for the amino acids are used. \ 
The symbol `x' is used for a position where any amino acid is accepted. \ 
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. \ 
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. \ 
Each element in a pattern is separated from its neighbor by a
`-'.  (Optional in fuzztran) \ 
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. \ 
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. \ 
A period ends the pattern. (Optional in fuzztran). \ 
For example, [DE](2)HS{P}X(2)PX(2,4)C"
]

integer: mismatch  [
  required: "Y"
  default: "0"
  minimum: "0"
  prompt: "Number of mismatches"
]

endsection: required

section: advanced [ info: "advanced Section" type: page ]
list: frame  [
  optional: "Y"
  default: "1"
  minimum: "1"
  maximum: "1"
  header: "Translation frames"
  values: "1:1, 2:2, 3:3, F:Forward three frames, -1:-1, -2:-2, -3:-3, R:Reverse three frames, 6:All six frames"
  delimiter: ","
  codedelimiter: ":"
  prompt: "Frame(s) to translate"
]

list: table  [
  optional: "Y"
  default: "0"
  minimum: "1"
  maximum: "1"
  header: "Genetic codes"
  values: "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"
  delimiter: ";"
  codedelimiter: ":"
  prompt: "Code to use"
]

endsection: advanced

section: output [ info: "output Section" type: page ]
report: outfile  [
  parameter: "Y"
  taglist: "int:mismatch=Mismatch int:frame=Frame int:start=PStart int:end=PEnd str:translation=Translation"
  rformat: "table"
  precision: 0
]

endsection: output

