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. 2007 Sep 12:8:333.
doi: 10.1186/1471-2105-8-333.

Integrating sequence and structural biology with DAS

Andreas Prlić  1 , Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kähäri, Tim J P Hubbard
Affiliations

Integrating sequence and structural biology with DAS

Andreas Prlić et al. BMC Bioinformatics. .

Abstract

Background: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.

Results: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources.

Conclusion: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.

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Figures

Figure 1
Figure 1
Example of the new DAS sources response. It provides meta description for DAS servers. The meaning of the different elements are: SOURCE: This DAS source provides mappings to protein structures for Ensembl proteins. It has a unique ID in the DAS registration server (DS_146). The doc_href provides a link to a web page with more documentation on this data. MAINTAINER: contact this person if there is a problem with the server, or if you have any questions about it. VERSION: this DAS source has been registered at the DAS registry in 2005 and provides the latest available data. COORDINATES: The data is served as annotations for the set of protein sequences provided by Ensembl. An example accession code is provided which can be used to check if the server is giving a valid response. CAPABILITIES: The DAS/1 features command is being supported by this server. The query uri field provides the location of the DAS source. PROP: Different labels can be assigned. The leaseTime is the last time when this server has been validated successfully.
Figure 2
Figure 2
We are providing a convention how to configure the display of different data-plots via the DAS stylesheet command. Here an example how this is used for plotting the scores of the signal peptide and transmembrane topology predictor Phobius [48], as well as hydropathicity data for the Suppressor of tumorigenicity protein 14 (Q9Y5Y6). The DAS features used in the three displays are exactly the same. The configuration is obtained from the stylesheet responses. The example can be also viewed via [49]. A) Using the stylesheet for histogram display. B) Using the stylesheet for lineplot display. C) Using the stylesheet for gradient display.
Figure 3
Figure 3
The Pfam DAS alignment viewer. Here, the first 20 sequences from the 14-3-3 [Pfam:PF00244] full alignment are requested from the pfamFullAlign DAS alignment server and displayed. The alignment is coloured according to the consensus of the whole alignment, which is provided as a DAS feature. The client allows simple paging through an alignment using the navigation buttons below the alignment.
Figure 4
Figure 4
SPICE displays a multiple structure alignment of the Saposins, as provided by the SISYPHUS database. It is possible to choose which of the structures should be superimposed and sequence features can be mapped on the three dimensional alignment. The top of the image shows the different DAS commands that are being used in order to obtain the integration of the data.
See this image and copyright information in PMC

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