Workflow Designer Documentation v. 1.18.0
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  • Search for TFBS

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This sample describes how to search for TFBS with a different methods and how to write the results into one output file.

First, the workflow reads sequences input by a user. Then, each sequence goes to searching TFBS elements. At that time two reading elements reads the matrix and model for TFBS searching and transfering this data into TFBS searching elements. After that the TFBS searching elements searches TFBS in the input sequences. After that the two data flows multiplexes into one output data flow. And finally, the multiplexed data are written into file, specified by a user.

You can configure the parameters of Search for TFBS with Weight Matrix, Search TFBS with SITECON and Multiplexer elements.

Tip
titleHow to Use This Sample

If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.

Workflow Sample Location

The workflow sample "Search for TFBS" can be found in the "Data Merging" section of the Workflow Designer samples.

Workflow Image

The workflow looks as follows:

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  <img src="/wiki/download/attachments/16122698/Search for TFBS.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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  <img src="/wiki/download/attachments/16122698/Search for TFBS_1.png"/>
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</center>

  2. Search for TFBS parameters: On this page you can modify search for TFBS parameters. 

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  <img src="/wiki/download/attachments/16122698/Search for TFBS_2.png"/>
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    The following parameters are available:

    Weight MatrixSemicolon-separated list of paths to the input files.
    Result annotationAnnotation name for marking found regions.
    Search inWhich strands should be searched: direct, complement or both.

    Min score

    		Minimum score to detect transcription factor binding site

     

    SITECON model

    		Semicolon-separated list of paths to the input files.

     

    Result annotation

    		Annotation name for marking found regions.

     

    Search in

    		Which strands should be searched: direct, complement or both.

     

    Min score

    		Minimum score to detect transcription factor binding site

     

    Min err1Alternative setting for filtering results, minimal value of Error type I.
    Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.
    Max err2Alternative setting for filtering results, max value of Error type II.
    Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.

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

    HTML
    <center>
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  <img src="/wiki/download/attachments/16122698/Search for TFBS_3.png"/>
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    The following parameters are available:

    Result file

     Location of output data file. If this attribute is set, slot "Location" in port will not be used.

    Accumulate results

    Accumulate all incoming data in one file or create separate files for each input.In the latter case, an incremental numerical suffix is added to the file name.