appl: est2genome [
  documentation: "Align EST and genomic DNA sequences"
  groups: "Alignment:Global"
  gui: yes
  batch: yes
  cpu: medium
]

section: input [ info: "input Section" type: page ]
seqall: est  [
  parameter: "Y"
  type: "dna"
  prompt: "EST sequence(s)"
]

sequence: genome  [
  parameter: "Y"
  type: "dna"
  prompt: "Genomic sequence"
]

endsection: input

section: advanced [ info: "advanced Section" type: page ]
integer: match  [
  optional: "Y"
  default: "1"
  information: "Score for matching two bases"
]

integer: mismatch  [
  optional: "Y"
  default: "1"
  information: "Cost for mismatching two bases"
]

integer: gappenalty  [
  optional: "Y"
  default: "2"
  information: "Gap penalty"
  help: "Cost for deleting a single base in either sequence, excluding introns"
]

integer: intronpenalty  [
  optional: "Y"
  default: "40"
  information: "Intron penalty"
  help: "Cost for an intron, independent of length."
]

integer: splicepenalty  [
  optional: "Y"
  default: "20"
  information: "Splice site penalty"
  help: "Cost for an intron, independent of length and starting/ending on donor-acceptor sites"
]

integer: minscore  [
  optional: "Y"
  default: "30"
  information: "Minimum accepted score"
  help: "Exclude alignments with scores below this threshold score."
]

bool: reverse  [
  information: "Reverse orientation"
  help: "Reverse the orientation of the EST sequence"
]

bool: splice  [
  default: "Y"
  information: "Use donor and acceptor splice sites"
  help: "Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false."
]

string: mode  [
  default: "both"
  information: "Comparison mode"
  help: "This determines the comparion mode. The default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparsion redone assuming a reversed (CT/AC) gene splicing direction. The other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand."
]

bool: best  [
  default: "Y"
  information: "Print out only best alignment"
  help: "You can print out all comparisons instead of just the best one by setting this to be false."
]

float: space  [
  default: "10.0"
  information: "Space threshold (in megabytes)"
  help: "for linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. \ If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM)"
]

integer: shuffle  [
  information: "Shuffle"
]

integer: seed  [
  default: "20825"
  information: "Random number seed"
]

endsection: advanced

section: output [ info: "output Section" type: page ]
outfile: outfile  [
  param: "y"
]

bool: align  [
  information: "Show the alignment"
  help: "Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown)."
]

integer: width  [
  default: "50"
  information: "Alignment width"
]

endsection: output

