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.
BioInformatics Center, National University of Singapore, Singapore. owu@bic.nus.edu.sg
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Wu
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Seow
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Wong
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Chung
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Subbiah
D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D016206:Databases, Bibliographic; D016208:Databases, Factual; D016239:MEDLINE; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011381:Programming Languages; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012846:Singapore; D012984:Software
D011506:Proteins; D004247:DNA