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

Parameters in GUI

both strands

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.
Pattern file	Load pattern from file in any sequence format or in newline-delimited format.
Use pattern name	If patterns are loaded from a file, use names of pattern sequences as annotation names. The name from the parameters is used by default.	False
Max Mismatches	Maximum number of mismatches between a substring and a pattern.	0
Search in	Specifies which strands should be searched: direct, complementary or both.	both strands
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.	Support ambiguous bases	Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered.	False
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

Qualifier name for pattern name

Name of qualifier in result annotations which is containing a pattern name.

pattern_name

Parameters in Workflow File

Type: search

Parameter	Parameter in the GUI	Type
result-name	Annotate as	string
pattern	Pattern(s)	string
pattern_file	Pattern file	string
use-names	Use pattern name	boolean
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 Translationallow-ins-del	Allow Insertions/Deletions	boolean
ambiguous	Support ambiguous bases	boolean
amino	Search in Translation	boolean
pattern-name-qual	Qualifier name for pattern name	string

Input/Output Ports

The element has 1 input port:

Name in GUI: Input data

Name in Schema File Workflow File: in-sequence

Slots:

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

And 1 output port:

Name in GUI: Pattern annotations

Name in Schema File Workflow File: out-annotations

Slots:

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