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Input sequence(s): On this page you must input sequence(s).
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Search for TFBS parameters: On this page you can modify search for TFBS parameters.
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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 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 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.
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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.
To try out this sample, add the input files to the Read Sequence element, select the Read Weight Matrix, Read SITECON model and select name and location of the output file in the Write Sequence element and run the workflow.
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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.