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. 2009 Jun 16;10 Suppl 6(Suppl 6):S18.
doi: 10.1186/1471-2105-10-S6-S18.

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

Affiliations

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

Alvaro Martínez Barrio et al. BMC Bioinformatics. .

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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Figures

Figure 1
Figure 1
Provirus structure. Based on the splice donor-acceptor sites, putative mRNA transcription for the retrovirus with simple replication strategies is shown. Putative viral genes with open reading frames: gag (MA, matrix; CA, capsid; NC, nucleocapsid); pro (PR, protease); pol (RT, reverse transcriptase; IN, integrase); env (SU, surface protein; TM, transmembrane protein). Other parts contained: PBS, primer binding site; SD, splice donor; SA, splice acceptor; PPT, polypurine tract.
Figure 2
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.
Figure 3
Figure 3
ERV present in the human genome (chr3:127092033,127100808) as displayed by EnsEMBL contigview in a track labeled herv_hg18 (placed at left part). A) After the DAS source was added and configured with features grouped B) Here the DAS source has been configured with ungrouped features and unlimited number of shown features. Color coded features can be appreciated (LTRs – royalblue; gag and motifs associated – yellow; pro and motifs – coral1; pol and motifs – springgreen; env and motifs – orange).
Figure 4
Figure 4
eBioX integration and visualization. 1–3) DAS directory service after some sources had been configured 4–5) Fetch entry menu and acceptor window 6) Annotation menu and acceptor window 7) eBioX outlines a view a retrovirus in the annotated region of the human genome (chr3:127092033,127100808).
Figure 5
Figure 5
Human transposon-free region hs11.65 overlapping endogenous retrovirus HERV:3233 in the human genome (chr11:5123000,5145000). The horizontal red bar represents hs11.65 (see labels in the left part of the figure). The protein coding gene OR52A1 with two alternative transcript forms is presented in blue and rust colors. The HERV:3233 annotated is displayed in a track called herv_hg18.

References

    1. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The Distributed Annotation System. BMC Bioinformatics. 2001;2:7–7. doi: 10.1186/1471-2105-2-7. - DOI - PMC - PubMed
    1. Lincoln D, editor. Distributed Annotation System (DAS) Version 1.53. Stein, Sean Eddy, Robin Dowell; http://www.biodas.org/documents/spec.html
    1. The BioSapiens project homepage http://www.biodas.org
    1. ENFIN:: a European Network of Excellence for Data Integration and Systems Biology http://www.enfin.org/page.php?page=home
    1. EMBRACE Network of Excellence http://www.embracegrid.info/

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