This sample workflow shows how to find substrings in input sequences, annotate them, and merge the found substring annotations with the original sequence annotations.
The steps of the workflow 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 "Find Substrings at Sequences" 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/16122696/Find Substrings at Sequences.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/16122696/Find Substrings at Sequences_1.png"/> <br> </center>
Input pattern(s): On this page you must input pattern(s).
<center> <br> <img src="/wiki/download/attachments/16122696/Find Substrings at Sequences_2.png"/> <br> </center>
Find substrings: On this page you can modify search and output parameters.
<center> <br> <img src="/wiki/download/attachments/16122696/Find Substrings at Sequences_3.png"/> <br> </center>
The following parameters are available:
|Annotate as||Name of the result annotations.|
|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.
Name of qualifier in result annotations which is containing a pattern name.
Maximum number of mismatches between a substring and a pattern.
Location of output data file. If this attribute is set, slot "Location" in port will not be used.
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.