SUPERFAMILY 1.75 HMM library and genome assignments server

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.