module Pwm: Biocaml_pwm
type int array array
Type to represent gap-free alignments. First dimension is
the sequence position, second dimension is for the alphabet.
Only DNA alphabet (A, C, G, T) is supported to rows should be
of length exactly four.
type float array
Probability distribution over an alphabet
val flat_background : unit -> background
Uniform distribution over A, C, G, T
val background_of_sequence : string -> float -> background
background_of_sequence seq pc estimates the base
frequency in seq using pc as pseudo-counts. Typical
value for pc is 0.1.
type float array array
Representation of a PWM
val make : count_matrix -> background -> t
Builds a PWM from a count_matrix and a background
val tandem : ?orientation:[ `direct | `everted | `inverted ] ->
spacer:int ->
count_matrix ->
count_matrix -> background -> t
tandem orientation spacer cm1 cm2 bg builds a PWM by constructing
a composite motif: it builds mat1 the PWM from cm1 under background bg
(resp. mat2 from cm2 under bg), then concatenates mat1 and mat2 with
spacer non scoring columns in between
val reverse_complement : t -> t
Reverse complement of a PWM
val scan : t -> string -> float -> (int * float) list
scan mat seq tol returns the list of positions (with
corresponding scores) such that the alignment score
of mat is superior to tol
val fast_scan : t -> string -> float -> (int * float) list
Identical to scan but directly implemented in C
val best_hit : t -> string -> int * float
best_hit mat seq returns the position and score of the best
alignment found in seq for the motif mat. Raise Invalid_arg
if seq is shorter than mat