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Title

A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation

Authors
Bucher, Philip
Published in Altman, R.; Brutlag, D.; Karp, P.; Lathrop, R.; Searls, D. International Conference on Intelligent Systems for Molecular Biology. Proceedings. Stanford University, Stanford (USA) - August 1994 - Menlo Park: AAAI Press. 1994, p. 53-61
Abstract A general syntax for expressing biomolecular sequence motifs is described, which will be used in future releases of the PROSITE data bank and in a similar collection of nucleic acid sequence motifs currently under development. The central part of the syntax is a regular structure which can be viewed as a generalization of the profiles introduced by Gribskov and coworkers. Accessory features implement specific motif search strategies and provide information helpful for the interpretation of predicted matches. Two contrasting examples, representing E. coli promoters and SH3 domains respectively, are shown to demonstrate the versatility of the syntax, and its compatibility with diverse motif search methods. It is argued, that a comprehensive machine-readable motif collection based on the new syntax, in conjunction with a standard search program, can serve as a general-purpose sequence interpretation and function prediction tool.
Keywords AnimalsBiopolymers/chemistryComputer SimulationHumansSequence AnalysisSoftware
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PMID: 7584418
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Research group Calipho (80)
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BUCHER, Philip, BAIROCH, Amos Marc. A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. In: Altman, R.; Brutlag, D.; Karp, P.; Lathrop, R.; Searls, D. (Ed.). ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Stanford University, Stanford (USA). Menlo Park : AAAI Press, 1994. p. 53-61. https://archive-ouverte.unige.ch/unige:36965

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Deposited on : 2014-05-27

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