Automated Querying of Genome Databases

Web-based, interactive querying of the genome databases has enabled the analysis of genomes in an integrated and visual manner that previously was difficult or impossible. However, many important biological questions cannot practically be answered using simple interactive methods that query only a single genomic location at a time. Addressing these questions requires batch- and programmatic database-querying. Although these approaches involve an initial, one-time cost of learning how to use the associated API and establishing an access method for programmed querying, the important capabilities they provide for addressing significant and otherwise relatively complex genomic questions often makes this effort well worthwhile. Moreover, as Web-based interfaces like Galaxy—which provide batch data acquisition and post-processing, but do not require programming—evolve, the powerful tools of genome-wide data analysis should become accessible to an ever wider range of biologists.