Bioinformatics.jl Documentation

Structure for sequence data.

function dotmatrix(s1::Sequence, s2::Sequence)

Calculate the dotplot matrix for given two sequences.

function edit_dist(s1::String, s2::String)

Calculate edit distance between two strings.

function frequency(seq::Sequence)

Count bases / amino acids for given sequence.

function gc_content(seq::Sequence, window_size::Int64)

Calculate GC-content of given sequence using a window.

function gc_content(seq::Sequence)

Calculate GC-content of given sequence.

function global_alignment_linear_gap(seq1, seq2, sm, d)

Needleman-Wunsch algorithm with linear gap penalty.

function gravy(seq::Sequence)

The GRAVY value for a peptide or protein is calculated as the sum of hydropathy values of all the amino acids, divided by the number of residues in the sequence.

See also: https://web.expasy.org/protparam/protparam-doc.html.

function hamming_dist(s1::String, s2::String)

Calculate Hamming distance between two strings.

function instability_index(seq::Sequence)

The instability index provides an estimate of the stability of your protein in a test tube.

See also: https://web.expasy.org/protparam/protparam-doc.html.

function minimum_skew(seq::Sequence)

Find genome positions where the skew is minimum.

function plot_dotmatrix(dotmatrix::Array{Int8})

Plot dotplot for given dotmatrix.

function plot_gc_content(seq::Sequence, window_size::Int64)

Plot GC-content of given sequence.

function possible_proteins(s::Sequence)

Find possible proteins of given sequence.

function protein_mass(seq::Sequence, type = "monoisotopic")

Calculate mass of given amino acid sequence.

function protparam(seq::Sequence)

Computes various physico-chemical properties that can be deduced from a protein sequence.

See also: https://web.expasy.org/protparam/protparam-doc.html.

function readFASTA(filename::String)

Parse a FASTA formatted file.

function reading_frames(s::Sequence)

Find all reading frames of given sequence.

function reverse_complement(s::Sequence)

Reverse complement of given DNA/RNA sequence.

function skew(seq::Sequence)

Calculate the skew values of sequence.

function skew_plot(seq::Sequence)

Plot skew diagram for given sequence.

function transcription(dna_seq::Sequence)

Transcribe DNA to RNA.

function translation(s::Sequence, start_pos::Int64 = 1)

Translate given DNA sequence to Amino Acid sequence.