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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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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.
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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.

Mentions: Simons et al. state that the human genome contains 856 transposon-free regions (TFRs) with a size over 10 kb and 9203 TFRs over 5 kb [45]. A complete ERV ranges between 7–11 kb long and is flanked on both sides by two long terminal repeats (LTRs) formed during reverse transcription. Our aim was to review if there would be any of the detected ERV among the predicted TFRs that would have been treated as a tandem repeat with all the internal provirus coding regions being considered as a simple TFR. In particular, we had our reservations about the predicted 10 kb TFRs since their size is very similar to typical ERVs. We downloaded a file linked at [46] describing human transposon-free regions (TFRs) in .bed format, parsed the hg18 coordinates reported and combined them into a request as a final test to our server, aiming to determine whether there were ERV annotations overlapping onto their predicted loci. The 10 kb regions were totally transposon free, none of our annotations overlapped. Interestingly, we found 15 ERVs which overlapped over as many 5 kb TFRs regions distributed in 7 different chromosomes (Additional File 1). These ERVs had an average score of 397 assigned by RetroTector. One of them, scoring as high as 722. HERV:3233 is placed in chromosome 11 and it is a typical HERV-H with gag, pol and env which indeed contains a fairly long open reading frame (ORF). The LTR divergence of the HERV-H element (41%) indicates an old integration in the genome. The human area (chr11:5123000,5145000), including the 6.2 kb TFR identified as hs11.65, is depicted in EnsEMBL (Figure 5) containing our annotation track by the .bed file annotations (Additional file 1).


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)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697641&req=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.
Mentions: Simons et al. state that the human genome contains 856 transposon-free regions (TFRs) with a size over 10 kb and 9203 TFRs over 5 kb [45]. A complete ERV ranges between 7–11 kb long and is flanked on both sides by two long terminal repeats (LTRs) formed during reverse transcription. Our aim was to review if there would be any of the detected ERV among the predicted TFRs that would have been treated as a tandem repeat with all the internal provirus coding regions being considered as a simple TFR. In particular, we had our reservations about the predicted 10 kb TFRs since their size is very similar to typical ERVs. We downloaded a file linked at [46] describing human transposon-free regions (TFRs) in .bed format, parsed the hg18 coordinates reported and combined them into a request as a final test to our server, aiming to determine whether there were ERV annotations overlapping onto their predicted loci. The 10 kb regions were totally transposon free, none of our annotations overlapped. Interestingly, we found 15 ERVs which overlapped over as many 5 kb TFRs regions distributed in 7 different chromosomes (Additional File 1). These ERVs had an average score of 397 assigned by RetroTector. One of them, scoring as high as 722. HERV:3233 is placed in chromosome 11 and it is a typical HERV-H with gag, pol and env which indeed contains a fairly long open reading frame (ORF). The LTR divergence of the HERV-H element (41%) indicates an old integration in the genome. The human area (chr11:5123000,5145000), including the 6.2 kb TFR identified as hs11.65, is depicted in EnsEMBL (Figure 5) containing our annotation track by the .bed file annotations (Additional file 1).

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.

Show MeSH
Related in: MedlinePlus