Until the recent advent of high-throughput experimental data-acquisition in biology, the computational analyssi 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 aprpoach" often resulted in piecemeal computational analysis with large amount of interventing "deadtime". The present high-throughput availability of experimental biological data requires a more streamlined and lintegrated "protocol approach". In this work, we illustrate such as 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 approch would re-phrase the same questions 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.
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