Find Substrings Element

Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.

Parameters in GUI

Parameter	Description	Default value
Annotate as (required)	Name of the result annotation.	misc_feature
Pattern(s)	Semicolon-separated list of patterns to search for. If this parameter is empty, the element uses the data prodused by Plain Text slot.
Max Mismatches	Maximum number of mismatches between a substring and a pattern.	0
Allow Insertions/Deletions	Takes into account possibility of insertions/deletions when searching. By default substitutions are only considered.	False
Search in	Specifies which strands should be searched: direct, complementary or both.	both strands
Search in Translation	Translates a supplied nucleotide sequence to protein and searches in the translated sequence.	False
Support ambiguous bases	Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered.	False

Parameters in Schema File

Type: search

Parameter	Parameter in the GUI	Type
result-name	Annotate as	string
pattern	Pattern(s)	string
max-mismatches-num	Max Mismatches	numeric
allow-ins-del	Allow Insertions/Deletions	boolean
strand	Search in	numeric Available values are: 0 - for searching in both strands 1 - for searching in direct strand 2 - for searching in complement strand
amino	Search in Translation	boolean
ambiguous	Support ambiguous bases	boolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input data

Name in Schema File: in-sequence

Slots:

Slot In GUI	Slot in Schema File	Type
Sequence	sequence	sequence
Plain text	text	string

And 1 output port:

Name in GUI: Pattern annotations

Name in Schema File: out-annotations

Slots:

Slot In GUI	Slot in Schema File	Type
Set of annotations	annotations	annotation-table