SUPERFAMILY Web Services
Distributed Annotation System
All SUPERFAMILY assignments are made available
through the Distributed Annotation System (DAS). The
DAS is a communication protocol
used to exchange biological sequence annotations. The DAS server offers the
oppurtunity to stay up to date with the SUPERFAMILY assignments without downloading
and installing database dumps. The SUPERFAMILY DAS server provides
protein domain assignment details in XML format for use by DAS clients such as
Ensembl,
gbrowse
(the gmod genome browser) and
DASTY.
Viewing SUPERFAMILY assigments on Ensembl
Ensembl
provide SUPERFAMILY protein domain assignments on their "protein view" pages.
The SUPERFAMILY assignment details are provided via our DAS server. The domain
visualisation is performed by Ensembl. For example, the following protein
features visualisation is produced by Ensembl for sequence
ENSP00000363868
from the Homo sapiens genome.
The protein features diagram shows that the
ENSP00000363868 sequence
contains two P-loop containing nucleoside triphosphate hydrolase
(SCOP ID 52540) domains.
Using the SUPERFAMILY DAS server
DAS requests take the form of URLs. For example, the SUPERFAMILY
annotation for ENSP00000363868
from Homo sapiens:
http://supfam.org/SUPERFAMILY/cgi-bin/das/hs/features?segment=ENSP00000363868
The DAS part of the URL starts with "/das". This is followed by the name of the data source, "/hs" (Homo sapiens).
The data sources correspond to the two character genome identifiers.
The next component is the command, "/features" which requests a list of features for the Homo sapiens genome.
Finally, this is followed by a query string, "?segment=ENSP00000363868" providing arguments to the command.
Other potentially useful commands include, "/dsn" for a list of data sources (genomes) available from the server,
http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn
"/types" for a list of annotation (superfamilies) available for sequences,
http://supfam.org/SUPERFAMILY/cgi-bin/das/hs/types
Additional DAS examples
The list of sequence entry points available and their sizes in base pairs. For Escherichia coli K12.
http://supfam.org/SUPERFAMILY/cgi-bin/das/ec/entry_points
Protein sequence corresponding to the indicated segment.
http://supfam.org/SUPERFAMILY/cgi-bin/das/hs/sequence?segment=ENSP00000363868
The DAS registry
The DAS registry
provides a list of all available DAS servers.
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