The extract annotations extension makes it very easy to extract annotations from one or more sequences. Using a few steps it is possible to extract e.g. all tRNA genes from the E. coli genome.
Moreover, it is possible to automatically add flanking regions for all the annotations which are found. It is also possible to search for specific words in all available annotations. When this plug-in is installed, annotations are extracted in this way:
select sequences | Toolbox in the Menu Bar | General Sequence Analyses | Extract Annotations
select sequences | right-click anyselected sequence | Toolbox | General Sequence Analyses | Extract Annotations
Extract annotations parameters
The parameters which can be set when extracting annotations are:
- Select annotation type to extract. From the drop-down box it is possible to specify which annotation type should be extracted from selected sequences. Only annotations which are found in the selected sequences are shown in the list.
- Search term. All annotations and attached information for each annotation will be searched for the entered term. If for instance you have a gene annotation called "HBG1" and another called "HBG2", you can extract both annotations by entering "HBG" in the search term field. When the annotation is of the type "gene", you have to select either "All" or "Gene" in the list. If you enter more than one word in the field, all the words will be used individually to search for annotations. E.g. typing "HBG1 HBG2" will match both annotations.
- Left flank. The output will include this number of residues to the left of the annotation.
- Right flank. The output will include this number of residues to the right of the annotation.
Only annotations that meet both search criteria - the annotation type and the search term - are extracted.
Output of extract annotations extension
This extension will generate a sequence list containing sequences carrying the annotation specified and including flanking regions.
Note! If large flanking regions are used, it it possible that two similar annotations are presented in the same output sequence.