Maximizing The Utility Of Avian Genomes With Comparative Genomics

DNA/RNA sequencing will transform every aspect of life sciences.  However, until algorithms can easily replace human thinking, the transformation of biological information into knowledge only happens in the minds of researchers.  In order for that promise to be fulfilled, biologists from all disciplines need to be armed with the analytical tools they find most useful to answer their research questions.  Helping to supply these scientists with the necessary computational resources are national cyberinfrastructure initiatives for the life sciences, and the iPlant Collaborative is one such example.  While nominally plant focused, the resources of iPlant are agnostic to the origin of biological data, work equally well on a variety of different organisms, and may be used to power additional analytical platforms.  One such platform is the web-based comparative genomics resource, CoGe, which houses nearly 20,000 genomes from over 15,000 organisms.  This talk will focus on the importance of having computational systems that are scalable and extensible with regards to both computational challenges and biological questions.  Examples using the genome of Gallus gallus and CoGe will identify syntenic regions between related avian and reptilian genomes, classify orthologs, characterize conserved non-coding sequences, and help identify large-scale patterns with highly fragmented, de novo assembled genomes.