= Profile hidden Markov model
A <profile hidden Markov model> represents the position-dependent structure of a <sequence alignment> using an ordered series of <match states> and optional <insertion states>, commonly with silent deletion states as well. An emitting state chooses one character from its <probability mass function>; transitions describe which profile position comes next. If deletion states are forbidden, an alignment column containing gaps cannot be a compulsory <match state>.
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