Filter Sequence That Match a Pattern

Using thist workflow you can select (or reject) only those sequence that match any pattern you input.

How 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.

The workflow sample "Filter Sequence That Match a Pattern" can be found in the "Scenarios" section of the Workflow Designer samples.

The workflow looks as follows:

The wizard has 3 pages.

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

The following parameters are available:

Pattern	Semicolon-separated list of patterns to search for.
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.