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Usage

Usage

BioAlignments.jl implements pairwise alignment algorithms. This is an example of globally aligning two amino acid sequences under an affine-gap scoding model:

using BioSequences
using BioAlignments
seq1 = aa"EPVTSHPKAVSPTETKPTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA"
seq2 = aa"EPSHPKAVSPTETKPTPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA"
model = AffineGapScoreModel(BLOSUM62, gap_open=-10, gap_extend=-1)
align = pairalign(GlobalAlignment(), seq1, seq2, model)
println(align)

BioAlignments.PairwiseAlignmentResult{Int64,BioSequences.BioSequence{BioSequences.AminoAcidAlphabet},BioSequences.BioSequence{BioSequences.AminoAcidAlphabet}}:
  score: 223
  seq:  1 EPVTSHPKAVSPTETKPT--EKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58
          ||  ||||||||||||||  || ||||||||||||| ||||||| |||||| |||| | |
  ref:  1 EP--SHPKAVSPTETKPTPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58

BioAlignments.jl also supports data formats for high-throughput sequencing technologies. The BAM file, one of the most commonly used file format to store aligned fragments, can be scanned as follows:

using BioAlignments
open(BAM.Reader, "data.bam") do reader
    for record in reader
        @show BAM.refname(record)
        @show BAM.position(record)
    end
end

BAM.refname(record) = "CHROMOSOME_I"
BAM.position(record) = 2