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Masking

Conservation masking

By default conservation masking is used, metazoan orthologues are retrieved and masking of underconserved residues is carried out. For more details see:

Davey NE, Shields DC & Edwards RJ (2009):
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics 25(4): 443-50.
[Bioinformatics.] [PubMed]



Feature masking

The web server allows masking of the input proteins, all formats can be masked based on disorder prediction by IUPRED and user-defined regions of interest, if the entry format is UniProt then defined features can be maskeds, areas such as transmembrane regions, protein domains and inaccessible residues can be masked as they are areas which have a low likelihood of containing motifs.

The same mechanism used for masking these region also allow the user identify specific regions of the proteins in which to confine the search , for example the user may wish to look at motifs which are occurring in the cytoplasmic regions of a set of proteins or may have prior knowledge of a region possibly containing a functional motif.

There are two types of masking in SLiMFinder Inclusive masking and Exclusive masking:
  • Inclusive masking will remove all of the sequence except the segment specified.
  • Exclusive masking will remove the segment specified.

Inclusive masking is preformed first. This means that exclusively masked regions appearing inside an inclusively masked region will be removed.

Masking is based on UniProt features, examples are:
SIGNALExtent of a signal sequence (prepeptide).
PROPEPExtent of a propeptide.
TOPO_DOMTopological domain.
TRANSMEMExtent of a transmembrane region.
DOMAINExtent of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.
REPEATExtent of an internal sequence repetition.
REGIONExtent of a region of interest in the sequence.
COILEDExtent of a coiled-coil region.
For example, [DOMAIN,TRANMEM] in the feature mask field will mask out Domain and Transmembrane regions annotated by Uniprot.