From sequence to structure to literature: the protocol approach to bioinformation

Until the recent advent of high-throughput experimental data-acquisition in biology, the computational analysis of the biological data was predominantly on an ad hoc basis--i.e., the application of a given piece of software on the biological data depended on the need of the moment. This "functional approach" often resulted in piecemeal computational analysis with large amount of intervening "dead-time". The present high-throughput availability of experimental biological data requires a more streamlined and integrated "protocol approach". In this work, we illustrate such a user-friendly protocol using a common question frequently faced by a wet-lab bench-biologist--"Now that I have a DNA or protein sequence, what can I do with it using a computer?" As phrased, this question is steeped in the functional approach. In contrast, the protocol approach would re-phrase the same question as "Now that I have a DNA or protein sequence, what can a computer do for me?" Our integrating tool can start with a sequence and build a substantial custom data-warehouse of computationally derived sequence information, structure information and relevant published literature, that is continually updated.