Figure 1.

A hidden Markov model of the generated signal in Illumina sequencing-by-synthesis platforms. An illustration of the graphical HMM of the Illumina’s sequencing platform. The observations yrepresent signal intensities after the removal of residual effects. The states are the combinations of <a onClick="popup('','MathML',630,470);return false;" target="_blank" href="">View MathML</a> and λt, which represent a subsequence of the template centered at position t and per-cluster density, respectively.

Shen and Vikalo BMC Bioinformatics 2012 13:160   doi:10.1186/1471-2105-13-160
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