HandlingGenomeData

Overview

This topic is intended to collect various useful tips, and real techniques employed to present genome data for analysis. The techniques will include use of genome analysis tools, description of appropriate data sources, management of datasets, updating relevant databases, and use within the GMOD GBrowse genome viewer tool.

Genome Analysis Tools

There are multiple genome data visualization tools, but probably three predominant user tools:

1. UCSC Genome Viewer
2. EnsEMBL Genome Suite
3. GMOD GBrowse genome browser
• Chado Database - tips and useful links for the Chado biological database

From the big three genome viewers, GBrowse has been implemented for our uses, but we highly recommend the UCSC browser as an authoritative alternate for avian genome data. The use of GBrowse here is intended to provide customized views, highly tailored to our specific purposes. The data content should be nearly identical in all genome tools, but is almost never perfect. The data here is inteded to represent the UCSC data alongside the growing set of complementary datasets, e.g. from expression experiments, HT sequencing studies, and custom gene and functional annotations. In this regard, hopefully GBrowse will enhance the existing data with flexible alternative views which are directly tied into active analysis work.

Bisque - Biological Simple Query Engine

The Bisque query engine was created to address several important issues:

• The need to capture and re-use optimized and/or very useful queries
• The need to run queries from other applications or scenarios, specifically...
• The desire to provide queries and reports via a web front-end
• The desire to call queries from a commandline, Perl, or R.
• The need for providing updated annotation data to the analysis pipeline.

The Bisque database is implemented in Postgresql, alongside the Chado Database.