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Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX.

Barrio AM, Lagercrantz E, Sperber GO, Blomberg J, Bongcam-Rudloff E - BMC Bioinformatics (2009)

Bottom Line: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data.The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution.Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Uppsala University, Biomedical centre, P,O, Box 598, SE-75124 Uppsala, Sweden. Alvaro.Martinez.Barrio@lcb.uu.se

ABSTRACT

Background: The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user.

Results: An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations.

Conclusion: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, http://www.dasregistry.org, or at http://loka.bmc.uu.se/das/sources.

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Left: Example of the DAS sources response in our server. To understand the configured meta-information of the DAS sources in our server, follow the legend in Figure I of Prlić et al., 2007. Right: Example of a DAS stylesheet response in our server. XML message shown only until TYPE level in order to distinguish better the different categories and types supported. The glyphs are folded into their respective types.
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Figure 2: Left: Example of the DAS sources response in our server. To understand the configured meta-information of the DAS sources in our server, follow the legend in Figure I of Prlić et al., 2007. Right: Example of a DAS stylesheet response in our server. XML message shown only until TYPE level in order to distinguish better the different categories and types supported. The glyphs are folded into their respective types.

Mentions: The visualization style was categorized into types according to the different parts that a retrovirus may incorporate (Figure 1). A description of our DAS source, the different categories and types for annotations is given in Figure 2. Every category and type was named according to the latest DAS style specification [41]. Inside each category, glyph forms and colors were chosen following the Document Type Definition (DTD) [42] stylesheet as accurately as it is possible to graphically represent retrovirus parts. Features are annotated at a chromosomal level for the NCBI_36 assembly of the Homo sapiens (Figure 2).


Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX.

Barrio AM, Lagercrantz E, Sperber GO, Blomberg J, Bongcam-Rudloff E - BMC Bioinformatics (2009)

Left: Example of the DAS sources response in our server. To understand the configured meta-information of the DAS sources in our server, follow the legend in Figure I of Prlić et al., 2007. Right: Example of a DAS stylesheet response in our server. XML message shown only until TYPE level in order to distinguish better the different categories and types supported. The glyphs are folded into their respective types.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697641&req=5

Figure 2: Left: Example of the DAS sources response in our server. To understand the configured meta-information of the DAS sources in our server, follow the legend in Figure I of Prlić et al., 2007. Right: Example of a DAS stylesheet response in our server. XML message shown only until TYPE level in order to distinguish better the different categories and types supported. The glyphs are folded into their respective types.
Mentions: The visualization style was categorized into types according to the different parts that a retrovirus may incorporate (Figure 1). A description of our DAS source, the different categories and types for annotations is given in Figure 2. Every category and type was named according to the latest DAS style specification [41]. Inside each category, glyph forms and colors were chosen following the Document Type Definition (DTD) [42] stylesheet as accurately as it is possible to graphically represent retrovirus parts. Features are annotated at a chromosomal level for the NCBI_36 assembly of the Homo sapiens (Figure 2).

Bottom Line: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data.The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution.Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Uppsala University, Biomedical centre, P,O, Box 598, SE-75124 Uppsala, Sweden. Alvaro.Martinez.Barrio@lcb.uu.se

ABSTRACT

Background: The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user.

Results: An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations.

Conclusion: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, http://www.dasregistry.org, or at http://loka.bmc.uu.se/das/sources.

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