How to use
You can specify the title of your request here. This is optional.
There are two ways to input a protein sequence:
I - If the protein is deposited in the UniProt database (either in SwissProt or TrEMBL) you can specify the accession
code or the ID of the protein in the "Enter SWISS-PROT/TrEMBL identifier or accession number" filed. The ANCHOR server
is always linked to newest version of UniProt. The header of the UniProt entry will be displayed as the title in the results page.
II - Type or cut and paste your sequence in the "paste the amino acid sequence" filed. The amino acid sequence must be in
the standard single letter code format. Spaces and other non-standard characters within the pasted sequence are permitted, however they
will be removed with the remaining sequence treated as a single continuous chain. If the first line starts with the ">" character
(e.g FASTA sequence headers) it will be used as the title in the results page. The minimum sequence length is 6 residues.
The recommended sequence format is
>Name of the sequence
There are three different prediction types offered, each using
different parameters optimized for slightly different applications. These are:
long disorder, short disorder, and structured domains.
The main profile of our server is to predict context-independent global disorder
that encompasses at least 30 consecutive residues of predicted disorder. For
this application the sequential neighbourhood of 100 residues is considered.
It uses a parameter set suited for
predicting short, probably context-dependent, disordered regions, such as
missing residues in the X-ray structure of an otherwise globular protein. For
this application the sequential neighbourhood of 25 residues is considered. As
chain termini of globular proteins are often disordered in X-ray structures,
this is taken into account by an end-adjustment parameter which favors
disorder prediction at the ends.
The dependable identification of ordered regions is a crucial step in target
selection for structural studies and structural genomics projects. Finding
putative structured domains suitable for stucture determination is another
potential application of this server. In this case the algorithm takes the
energy profile and finds continuous regions confidently predicted ordered.
Neighbouring regions close to each other are merged, while regions shorter
than the minimal domain size of at least 30 residues are ignored. When this
prediction type is selected, the region(s) predicted to correspond to
structured/globular domains are returned.
Raw data only:
This offers a simple text output. For predicition types "local" and "global"
disorder there is a line corresponding to each residue, specifying its
sequential number, residues type, and its score. This score can be between 0
and 1. Scores above 0.5 indicate disorder. If the prediction type "structured
domains" was selected, only the sequence is returned, with uppercase letters
indicating putative globular domains.
Beside the text output, a graphical image (a png file) is generated using
JpGraph softwer. Large sequences
are chopped into smaller fragments. The user can change the window size of this
plot. If the prediction type "structured domains" was selected, the corresponding
regions are indicated by thick lines on the graph.