@*~RSC_HELP_SEQFEAT
Residue annotation from services
Sequence features are annotations of sequence positions indicating for example signal peptides, disulfide bonds,
glycosylated or phosphorylated amino acids. In
Strap they are loaded from the sequence file, from UniProt or from the
Catalytic Site Atlas at the EBI.
They used to be loaded also from BioDAS* servers, until BioDAS became unavailable.
Annotated sequences are underlined in the alignment
panel and in the alignment output. They have a context menu
(right-click), a balloon message and they can be dragged to other sequences or 3D-views.
Loading residue annotations from servers
The Table
The table lists the residue annotations of all sequences. Each
table row gives the color, the name such as "Metal binding".
With check-boxes in each row the user can control where they are displayed.
The following explains the table columns in detail:
- Name: This column tells the type of sequence feature. Left click
selects all annotations of this type. In the alignment panel the
selected residue annotations will be indicated by WIKI:Marching_ants. Right
click opens the context menu for the residue annotations. Drag-and-drop copies all residue annotations of this type to
the target such as a 3D-structure.
- #: The number of entries found.
- Navigation: Jump to the first | next | previous | last selected residue in the alignment panel.
Colors
Each annotation type has a color for black background (screen), and one for white background (paper).
These colors can be customized in the context menu.
Mouse-control
The following mouse actions apply to the residue annotation in the table and in the alignment panel.
- Right click opens a context menu for the feature.
- Ctrl+left-click selects and deselects the residue annotations.
- Dragging the mouse copies residue annotations to other sequences or to 3D-views (See WIKI:Drag_and_drop).
- Double clicking a feature opens a table with detailed data. The user can add annotation entries which are persistent.
- Moving the mouse provides a balloon text with information on the sequence feature under the mouse.
Deactivated annotations
Deactivated annotations are hidden.
Reasons why annotations are deactivated:
- Poor alignment with the homologous sequence, where the feature is indirectly inferred from.
- The Sequence positions are outside the shown sequence fragment. This is often the case for
N-terminal signal sequences in Pfam alignments showing only the conserved part.
- Secondary structure when the structure information is already obtained from the sequence
file.
- Phospho-tyrosine falling on a non-'Y' residue. This is controlled by the third column of the
color table which contains a set of allowed letters or a dash if all letters are allowed. This table appears when
opening the menu item Edit > Color of the context menu.
Examples
The following SwissProt entries have many annotations and can be used for testing/demonstration:
UNIPROT:Q9Y4K3 UNIPROT:Q9H9D4 UNIPROT:Q05516 UNIPROT:P28825 UNIPROT:P08045 UNIPROT:Q13105
#if CPP_DEACTIVATED
ftp://ftp.psb.ugent.be/pub/ssb/so.rdf.gz
Todo Q9UHG2 Peptide and region
s8stdout -align=UNIPROT:hslv_ecoli -script="uniprot_features * "
#endif //CPP_DEACTIVATED
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