Module Biocaml_pwm (.ml)

module Biocaml_pwm: sig .. end

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.

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