Reference

aa2int(seq::String[])

Given a vector of string amino-acid sequences, converts it to an integer matrix.

aa2int(seq::String)

Convert a string amino-acid sequence to a vector of integers.

aa2int(char)

Amino-acid one-letter code to integer (1 to 21, with gap = 21).

conservation_matrix(P, M; unit = log(2))

Similar to conservation_matrix(P), but instead of a flat measure over letters at each site, computes a KL divergence to a prior measure M.

conservation_matrix(P; unit = log(2))

Given a matrix of frequencies P of size (q, L), where q is the number of possible letters and L the sequence length, returns the matrix of conservations (as defined by Schneider and Stephens 1990, 10.1093/nar/18.20.6097).

conservation_scores(P, M; unit = log(2))

Similar to conservation_scores(P), but instead of a flat measure over letters at each site, computes a KL divergence to a prior measure M.

conservation_scores(P; unit = log(2))

Conservation scores at each site. The default unit = log(2) gives results in bits.

int2aa(i)

Get the amino acid (in one letter code) corresponding to the integer i.

letter_at(letter, color, (x, y), yscale)

Adds a letter to the current plot, at the given position.

logo_from_matrix(weights, alphabet)

Construct a SequenceLogo from a weight matrix of size (q, L), where q is the number of possible letters and L the length of the sequence. alphabet is a String containing the q possible letters.

plot_sequence_logo(sequence_logo, color_fun; thresh=0)

Plots a sequence logo. Ignores letters with weights smaller than thresh.

remove_duplicate_letters(logo)

Removes duplicate letters at each site (summing their weights).

sort_letters(site)

Sorts the letters in a site in order of increasing absolute weight.

sort_letters(logo; remove_duplicates=true)

Sorts the letters in all sites in order of increasing absolute weight.