This sample shows how to search for transcription factor binding sites (TFBS) using two different approaches - weight matrices and SITECON models - and write the found TFBS annotations into one output file.
The workflow steps are these:
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
The workflow sample "Search for TFBS" can be found in the "Data Merging" section of the Workflow Designer samples.
The workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/16122698/Search for TFBS.png"/> <br> </center> |
The wizard has 3 pages.
Input sequence(s): On this page you must input sequence(s).
<center> <br> <img src="/wiki/download/attachments/16122698/Search for TFBS_1.png"/> <br> </center> |
Search for TFBS parameters: On this page you can modify search for TFBS parameters.
<center> <br> <img src="/wiki/download/attachments/16122698/Search for TFBS_2.png"/> <br> </center> |
The following parameters are available:
Weight Matrix | 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
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SITECON model | Semicolon-separated list of paths to the input files.
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Result annotation | Annotation name for marking found regions.
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Search in | Which strands should be searched: direct, complement or both.
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Min score | Minimum score to detect transcription factor binding site
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Min err1 | Alternative 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 err2 | Alternative 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. |
Output data: On this page you can modify output parameters.
<center> <br> <img src="/wiki/download/attachments/16122698/Search for TFBS_3.png"/> <br> </center> |
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. |