So I've read a few threads on here... and it seems that there are quite a few questions about what SPECIFICALLY makes up a hidden markov model:
... I'll do my very best to present this information clearly ...
(please correct any of this explicitly if its incorrect ... or just correct it, as I've made this a community wiki. )
Application of HMMs is to compare a reference genome, to one currently being assembled.
NOT in the manner which the current nucleotide is the sole determinant of the next in the sequence. Which is incorrect even if we're talking from the amino acid standpoint ( IE 3 base pairs ) ... see http://biostar.stackexchange.com/questions/1221/when-can-a-markov-model-be-described-as-hidden. Right? ... ok.
1) Memoryless means it is not influenced by the previous sequences ( finding / states / residues / determinations / whatever the previous "items" were ) ... How can one say that the evolutionary precursors to a genomic sequence have "no impact"? ...
NOTE: It makes sense that the entire gamut of evolution which lead up to that genome ... would influence it
2) Specifically what makes gives this process its designation of "hidden" ( in "Hidden Markov Model" ) ? As mentioned in this post: http://biostar.stackexchange.com/questions/1221/when-can-a-markov-model-be-described-as-hidden
It is stated ( from wiki link ) that "the state is not directly visible, but output, dependent on the state, is visible."
NOTE: The sequence is there and we're reading it with some process... there is nothing "hidden" about this.
Does the "hidden" refer to not knowing the evolutionary process which placed that nucleotide there?
Does the "hidden" designation refer to some process-dependent applications... say sequencing done by fluorescing molecules ( which would be indicative of a specific nucleotide ) ... but not a "direct read"
"direct read" as meaning "Yes unequivocally , this is a Cytosine molecule here" ... not by perception of causal relation ... but instead by "directly reading"
Please Specifically label and answer questions 1 and 2 =]