Document Type
Article
Publication Date
1-18-2016
Publication Title
Evolutionary Bioinformatics
Volume
2016
Issue
12
Pages
23-37
Publisher Name
Libertas Academica
Abstract
As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 sequences. Phylogenetic analyses were conducted for >6,000 HIV-1 sequences revealing spatial and temporal factors influence the evolution of the individual genes uniquely. Nevertheless, signatures of origin can be extrapolated even despite increased globalization. The approach developed here can easily be customized for any species of interest.
Recommended Citation
Steven Reisman and Thomas Hatzopoulos and Konstantin Läufer and George K. Thiruvathukal and and Catherine Putonti, A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1, Evolutionary Bioinformatics 2016:12 23-27, doi:10.4137/EBO.S32757.
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Comments
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