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In this group you can specify where to search for a pattern: in what region and in which strand (for nucleotide sequences). Also for nucleotide sequences, it is possible to search for a pattern on the sequence translations.

Strand — for nucleotide sequences only. Specifies on which strand to search for a pattern: DirectReverse-complementary, or Both strands.

Search in — for nucleotide sequences you can select the Translation value for this option. In this case, the input pattern will be searched in the amino acid translations.


In the Save annotation(s) to group, you can set up a file to store annotations.  It could be either an existing annotation table object or a new annotation table.

In the Annotation parameters group, you can specify the name of the group and the name of the annotation. If the group name is set to <auto> UGENE will use the group name as the name for the group. You can use the ‘/’ characters in this field as a group name separator to create subgroups. If the annotation name is set to by type UGENE will use the annotation type from the Annotation type: table as the name for the annotation. Also you can add a description in the corresponding text field. To use a pattern name for the annotations check the corresponding checkbox.

After that click the Create annotations button. The annotations will be created. Also you can see the result statistic and navigation under the Search for: field:



     <img src="/wiki/download/attachments/10289539/Annotations settings_1_1.png"/>

Searching for one or several patterns and names of the result annotations

If you search for one pattern only, than then input the required name into the Annotation name field and leave the Use pattern name check box  checkbox unchecked.

You can also search for several patterns at a time by:


  • Inputting several patterns into the search filed in FASTA format:
  • Loading patterns from a FASTA file

Even when you search for several patterns, the names of the found annotations will be identical by default (the name is specified in the Annotation name field).

If you want to assign different names to annotations found for different patterns, than then you should:

  • Input the patterns in FASTA format (the latter two cases above)
  • Check the Use pattern name checkbox in the Annotation parameters group