#!UGENE_WORKFLOW
#
workflow "New schema"{
read-sequence {
type:read-sequence;
name:"Read sequence";
merge-gap:10;
mode:0;
}
ssearch {
type:ssearch;
name:"Smith-Waterman Search";
algorithm:"Classic 2";
amino:false;
filter-strategy:filter-intersections;
gap-ext-score:-1;
gap-open-score:-10;
matrix:Auto;
min-score:90;
result-name:misc_feature;
strand:both;
}
write-annotations {
type:write-annotations;
name:"Write annotations";
annotations-name:"unknown features";
document-format:genbank;
write-mode:2;
}
read-sequence.sequence->ssearch.in-sequence.sequence
ssearch.annotations->write-annotations.in-annotations.annotations
.iteration "Default iteration1"{
id:13;
ssearch {
pattern:ATGACGGGCCAAACGGTAACGTTAAAGGAT;
result-name:Primer1;
}
read-sequence {
url-in:Sequence.gb;
}
write-annotations {
url-out:annotation1.gb;
write-mode:1;
}
}
.iteration "Default iteration2"{
id:14;
ssearch {
pattern:CAGATGAAACTGTGGCTCCCTCAGGCGCCAC;
result-name:Primer2;
}
read-sequence {
url-in:Sequence.gb;
}
write-annotations {
url-out:annotation2.gb;
write-mode:1;
}
}
.iteration "Default iteration3"{
id:15;
ssearch {
pattern:TATTACTAGTAATGTTGATGTAAAAGCC;
result-name:Primer3;
}
read-sequence {
url-in:Sequence.gb;
}
write-annotations {
url-out:annotation3.gb;
write-mode:1;
}
}
.meta {
visual {
read-sequence {
description:" Read sequence
Reads sequence(s) from Sequence.gb.
";
tooltip:"Reads sequences and annotations if any from local or remote files.";
pos:"-900 -915";
style:ext;
bg-color-ext:"0 128 128 64";
out-sequence.angle:360;
}
ssearch {
description:" Smith-Waterman Search
Searches regions in each sequence from Read sequence similar to ATGACGGGCCAAACGGTAACGTTAAAGGAT pattern(s).
Percent similarity between a sequence and a pattern is 90%.
Seaches in both strands of a sequence.
Outputs the regions found annotated as Primer1.
";
tooltip:"Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations. Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment.";
pos:"-720 -915";
style:ext;
bg-color-ext:"0 128 128 64";
in-sequence.angle:180;
out-annotations.angle:360;
}
write-annotations {
description:"
Write annotations
Save all annotations from Smith-Waterman Search to annotation1.gb in genbank format
";
tooltip:"Writes all supplied annotations to file(s) in selected formatId.";
pos:"-405 -915";
style:ext;
bg-color-ext:"0 128 128 64";
in-annotations.angle:180;
}
read-sequence.out-sequence->ssearch.in-sequence {
text-pos:"-27.5 -24";
}
ssearch.out-annotations->write-annotations.in-annotations {
text-pos:"-45 -37";
}
}
}
}