layout: specifies the layout of vertices (nodes). See function mctosc for more information on the transformation. Too often, piling more reality onto a fragile ad hoc program makes it collapse under its own weight. x: A hidden Markov model object of class hmm created with buildhmm (or buildmm).Multichannel hmm objects are automatically transformed into single-channel objects. The moment we perfect our ad hoc genefinder, we wish we had also modeled translational initiation consensus, alternative splicing and a polyadenylation signal. 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. How should these parameters be set? How should different kinds of information be weighted? A second issue is to interpret results probabilistically. A genefinder, for instance, ought to combine splice-site consensus, codon bias, exon/ intron length preferences and open reading frame analysis into one scoring system. One is that we want to incorporate heterogeneous sources of information. We can always write an ad hoc program for any given problem, but the same frustrating issues will always recur. In sequence alignment, we want to associate residues in a query sequence with homologous residues in a target database sequence. In gene identification, we want to label nucleotides as exons, introns, or intergenic sequence. Often, biological sequence analysis is just a matter of putting the right label on each residue.
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