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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
Published on: March 22, 2016
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and
Alvaro Martínez Barrio1, Erik Lagercrantz, Göran O Sperber
1The Linnaeus Centre for Bioinformatics, Uppsala University, Biomedical centre, P,O, Box 598, SE-75124 Uppsala, Sweden. Alvaro.Martinez.Barrio@lcb.uu.se
BMC Bioinformatics
|June 19, 2009
Summary
A new annotation server using the Distributed Annotation System (DAS) protocol effectively shares endogenous retrovirus (ERV) data. This facilitates integrated analysis of ERV genomic contributions to evolution.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- The Distributed Annotation System (DAS) is a key network protocol for sharing biological data.
- DAS enables integrated views by connecting sequence data with annotations from various servers.
Purpose of the Study:
- To develop a DAS annotation server for endogenous retroviruses (ERVs) detected by RetroTector.
- To demonstrate the implementation of DAS 1.5 protocol for constructing annotation servers.
Main Methods:
- Implemented DAS 1.5 protocol commands for server construction.
- Separated data distribution from visualization using the eBioX program.
- Utilized RetroTector for in silico detection and annotation of ERVs.
Main Results:
- Successfully created and exemplified a DAS annotation server for ERV data.
- Demonstrated visualization of ERVs in two DAS clients via eBioX.
- Enabled rapid analysis of genomic regions lacking retroviral insertions.
Conclusions:
- The DAS protocol is effective for distributing endogenous retrovirus data.
- DAS aids in combining genome-wide annotation and visualization for evolutionary studies.
- eBioX integrates DAS reference/annotation servers for enhanced ERV data visualization.
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