The document discusses the Karyotype DAS client, which provides an interactive web client for visualizing and comparing genome annotations from different DAS sources. It summarizes the Distributed Annotation System (DAS) protocol, which allows for distributed genome annotations across multiple independent databases viewed together. The Karyotype DAS client is presented as a solution for exploring genome information and annotations in their full genomic context. Researchers can integrate their own annotations and analysis results by making them accessible via the virtual DAS registry.

1. Karyotype DAS client
APBC2009
Rafael C. Jimenez (rjimenez@cipf.es), Joaquin Tarraga, Ignacio Medina, Eva Alloza and Joaquin Dopazo
P67
Large centralized databases like GenBank or specialized curated databases
such as Swissprot have been used as solution to store and share genome and
protein information. However as new technologies allow for a faster
production of data, updating and maintaining annotations in centralized
repositories has become increasingly difficult even for large organizations.
The Distributed Annotation System (DAS) introduces a well-defined
communication protocol motivated by the idea that annotations should not
remain on a single centralized database, but should instead rely on a
federated system: a logical association of independent sources spread over
multiple sites that provides a single, integrated and coherent view of all
resources in the federation.
Microarrays, DNA Sequencing and other large-scale genomic technologies are
now routinely used to generate a vast amount of genomic profiles. Exploratory
analysis of this data is crucial in helping to understand the data and create
new biological hypotheses. This requires integration of multi-dimensional
genome analysis in context with related genome information and an effective
integrative visualization. The DAS protocol provides a platform to distribute
genome annotation through DAS servers, discover DAS sources using the
DAS registry and integrate and visualize distributed annotations utilizing a
proper client.
DAS is a widely adopted standard protocol. It has been embraced by
centralized databases like Ensembl and Uniprot to provide and share genome
and protein information. Genome browsers like Gbrowse, the UCSC browser
and the Ensembl Browser have adopted the protocol accessing third party
sources and displaying their content in a genomic context. The applicability of
DAS is also extended to protDASein sequence and structure data integrating
major protein databases like CATH, SCOP, MSD, InterPro, and Pfam. DAS
clients like SPICE and Dasty query DAS sources to display protein annotations
and related 3D structure and genome information.
sources and displaying their content in a genomic context. The applicability of
DAS is also extended to protDASein sequence and structure data integrating
major protein databases like CATH, SCOP, MSD, InterPro, and Pfam. DAS
clients like SPICE and Dasty query DAS sources to display protein annotations
and related 3D structure and genome information.
DAS genome browsers are specialized to concentrate on derived features over
specific genome regions, in particular, gene structures and protein
sequences. However these systems are not designed for visually representing
features on a higher level of genome compaction. Interpretation of genome
information like copy number aberrations requires viewing the data in its full
genomic context. Thus, such genome browser do not employ an effective
exploratory visualization on a higher representation level.
As a solution we propose an exploratory information approach to integrate
genome information and make it readily visible in a manner that allows easy
interpretation of their full genomic context. We have developed a Karyotype
DAS client, a highly interactive web client to aid researchers to visualize,
share and compare annotations coming from DAS sources and genome
analysis DAS results. To aid researchers to include exploratory analysis and
tailored functional genomics results we are working on the next version of
GEPAS (The Gene Expression Profile Analysis Suite) to offer results in DAS
format. Moreover we have created a virtual DAS registry which allows
researchers with little knowledge about DAS to make their custom annotations
accessible in DAS format. Thus, researchers can integrate their annotations
and analysis results on our DAS client or any of the other DAS browsers.
Abstract
Results
As an example the Karyotype viewer includes a view of annotations from the TCAG’s Database of
Genomic Variants (DGV)—known as “the Toronto Database” (turquoise blue), from a file of selected
micro RNA (blue), from a aCGH annotations (yellow) and from sequencing data (red). We selected the
former source from the DAS Registry while the other sources are made available through the virtual
DAS registry.
DASRegistryVirtualDASRegistry
KaryotypeDASviewer