Bioinformatics - BioinformaticsAn Introduction for Computer...

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Bioinformatics—An Introduction for Computer Scientists JACQUES COHEN Brandeis University Abstract. The article aims to introduce computer scientists to the new feld oF bioinFormatics. This area has arisen From the needs oF biologists to utilize and help interpret the vast amounts oF data that are constantly being gathered in genomic research—and its more recent counterparts, proteomics and Functional genomics. The ultimate goal oF bioinFormatics is to develop in silico models that will complement in vitro and in vivo biological experiments. The article provides a bird’s eye view oF the basic concepts in molecular cell biology, outlines the nature oF the existing data, and describes the kind oF computer algorithms and techniques that are necessary to understand cell behavior. The underlying motivation For many oF the bioinFormatics approaches is the evolution oF organisms and the complexity oF working with incomplete and noisy data. The topics covered include: descriptions oF the current soFtware especially developed For biologists, computer and mathematical cell models, and areas oF computer science that play an important role in bioinFormatics. Categories and Subject Descriptors: A.1 [ Introductory and Survey ]; ±.1.1 [ Computation by Abstract Devices ]: Models oF Computation— Automata (e.g., fnite, push-down, resource-bounded) ;±.4.2 [ Mathematical Logic and Formal Languages ]: Grammars and Other Rewriting Systems; G.2.0 [ Discrete Mathematics ]: General; G.3 [ Probability and Statistics ]; H.3.0 [ Information Storage and Retrieval ]: General; I.2.8 [ Arti±cial Intelligence ]: Problem Solving, Control Methods, and Search; I.5.3 [ Pattern Recongnition ]: Clustering; I.5.4 [ Pattern Recongnition ]: Applications— Text processing ; I.6.8 [ Simulation and Modeling ]: Types oF Simulation— Continuous; discrete event ; I.7.0 [ Document and Text Processing ]: General; J.3 [ Life and Medical Sciences ]: Biology and genetics General Terms: Algorithms, Languages, Theory Additional Key Words and Phrases: Molecular cell biology, computer, DNA, alignments, dynamic programming, parsing biological sequences, hidden-Markov-models, phylogenetic trees, RNA and protein structure, cell simulation and modeling, microarray 1. INTRODUCTION It is undeniable that, among the sciences, biology played a key role in the twentieth century. That role is likely to acquire Fur- ther importance in the years to come. In the wake oF the work oF Watson and Crick, Author’s address: Department oF Computer Science, Brandeis University, Waltham, MA 02454; email: jc@ cs.brandeis.edu. Permission to make digital/hard copy oF part or all oF this work For personal or classroom use is granted without Fee provided that the copies are not made or distributed For proft or commercial advantage, the copyright notice, the title oF the publication, and its date appear, and notice is given that copying is by permission oF ACM, Inc. To copy otherwise, to republish, to post on servers, or to redistribute to lists requires prior specifc permission and/or a Fee.
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This note was uploaded on 07/30/2011 for the course COP 4810 taught by Professor Staff during the Spring '11 term at University of Central Florida.

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Bioinformatics - BioinformaticsAn Introduction for Computer...

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