How should these parameters be set how should

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Unformatted text preview: ow should these parameters be set? How should different kinds of information be weighted? A second issue is to interpret results probabilistically. Finding a best scoring answer is one thing, but what does the score mean, and how confident are we that the best scoring answer is correct? A third issue is extensibility. The moment we perfect our ad hoc genefinder, we wish we had also modeled translational initiation consensus, alternative splicing and a polyadenylation signal. Too often, piling more reality onto a fragile ad hoc program makes it collapse under its own weight. Hidden Markov models (HMMs) are a formal foundation for making probabilistic models of linear sequence ‘labeling’ problems1,2. They provide a conceptual toolkit for building complex models just by draw- Sean R. Eddy is at Howard Hughes Medical Institute & Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., Box 8510, Saint Louis, Missouri 63108, USA. e-mail: eddy@genetics.wustl.edu A = 0.25 C = 0.25 G = 0.25 T = 0.2...
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