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Module Biocaml_pwm (.ml)

Position-weight matrix

This module can be used to create position-weight matrices (PWM) to describe a DNA motif. Such matrices can then be searched on a DNA sequence, given a threshold for alignment score.

module Biocaml_pwm:
sig
type count_matrix = 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 background = private 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 t = private 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
end