A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1.

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 fact

SUBMITTER: Reisman S 

PROVIDER: S-EPMC4718148 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature