Annotation
PIPprofileR is able to use an annotation file to allow :
- the specific search of a PIP profile for a given feature (documentation) ;
- Enrich the exploration of the PIP profile over the complete sequence (documentation).
The application is able to import several types of annotation files:
- GFF3, GFF2/GTF (more information about the format: here)
- bed (more information about the format: here).
Figure 1 | Screenshot of the annotation file import
When you import an annotation file as a GGF3 file (available here), a preview of the import is offered (Figure 2).
Figure 2 | Preview of GFF3 file
This preview represents exactly how the application will read the file and therefore allows to anticipate possible reading problems. An example is shown in figure 3 with the reading of a file containing sequences in fasta format. You can get more help by clicking on "more" (scroll down figure 3). To test this functionality, you have at your disposal an error file: here.
Figure 3 | Import error
When the annotation file has been imported, a new tab appears in the sidebar: Annotation.
A table is available with several functionalities (Figure 4) :
- Column filtering ;
- Content search ;
- Link to reference databases (such as NCBI).
Figure 4 | Example of annotation exploration