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This simple workflow finds patterns in you sequences and save them as annotations. You can use the workflow to map primers, regulatory signals, genes, etc. It loads any set of sequences from your files or folders and finds patterns in them. 

Workflow Sample Location

The workflow sample "Find Patterns" can be found in the "Scenarios" section of the Workflow Designer samples.

Workflow Image

The workflow looks as follows:

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  <img src="/wiki/download/attachments/16122733/Find Patterns.png"/>
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Workflow Wizard

The wizard has 3 pages.

1. Input sequence(s): On this page you must input sequence(s). 

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   <center> <br> <img src="/wiki/download/attachments/16122733/Find Patterns_1.png"/> <br> </center>

2. Find pattern: On this page you must input pattern(s) and you can modify searching parameters. 

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   <center> <br> <img src="/wiki/download/attachments/16122733/Find Patterns_2.png"/> <br> </center>

   The following parameters are available:

   Pattern	Semicolon-separated list of patterns to search for.
   Annotate as	Name of the result annotations.
   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.
   Max Mismatches	Maximum number of mismatches between a substring and a pattern.
   Allow Insertions/Deletions	Takes into account possibility of insertions/deletions when searching. By default substitutions are only considered.
   Search in Translation	Translates a supplied nucleotide sequence to protein and searches in the translated sequence.
   Support ambiguous bases	Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered.
   Qualifier name	Name of qualifier in result annotations which is containing a pattern name.

3. Output data: On this page you can modify output parameters. 

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   <center> <br> <img src="/wiki/download/attachments/16122733/Find Patterns_3.png"/> <br> </center>