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dinucleotidic pwm #4

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erivals opened this issue Jan 26, 2023 · 1 comment
Open

dinucleotidic pwm #4

erivals opened this issue Jan 26, 2023 · 1 comment

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@erivals
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erivals commented Jan 26, 2023

Dear Shane,

PWMs consider column of the alignment as independent from each other.
A dinucleotidic pwm (di-PWM) uses 2 columns (a dinucleotide) to compute the score and thus introduce a dependency between adjacent columns. The score computation differs a bit and the score distribution also from that of a PWM.

Could you consider to adapt or generalize your code for di-PWMs ?

best
Eric
@kchu25
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kchu25 commented Jan 26, 2023

Dear Eric,

My time is a bit tight. Are you considering the statistically significant matched strings from higher-ordered PWMs? In that case, I believe one of the most sophisticated methods to this date is MOODS (check their github and documentation), for which they take into account first-ordered PWMs with .adm files.

best,
Shane

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@erivals @kchu25