bio-alignment

Alignment handler for multiple sequence alignments (MSA).

This alignment handler makes no assumptions about the underlying sequence object. Support for any nucleotide, amino acid and codon sequences that are lists. Any list with payload can be used (e.g. nucleotide quality score, codon annotation). The only requirement is that the list is iterable and can be indexed.

This work is based on Pjotr's experience designing the BioScala Alignment handler and BioRuby's PAML support. Read the Bio::BioAlignment design document for Ruby.

Note: this software is under active development.

Developers

Codon alignment example

To use the library, load aligned sequences into the Alignment matrix. Here we write an amino acid alignment from a codon aligmment (note codon gaps are represented by '---')

  require 'bio-alignment'
  require 'bigbio' # Fasta reader and writer

  aln = Alignment.new
  fasta = FastaReader.new('codon-alignment.fa')
  fasta.each do | rec |
    aln.sequences << CodonSequence.new(rec.id, rec.seq)
  end
  # write a matching amino acid alignment
  fasta = FastaWriter.new('aa-aln.fa')
  aln.rows.each do | row |
    fasta.write(row.id, row.to_aa.to_s)
  end

Pal2nal

A protein (amino acid) to nucleotide alignment would first load the sequences

  aln1 = Alignment.new
  fasta1 = FastaWriter.new('aa-aln.fa')
  aln1.rows.each do | row |
    fasta1.write(row.id, row.to_aa.to_s)
  end
  aln2 = Alignment.new
  fasta2 = FastaReader.new('nt.fa')
  fasta2.each do | rec |
    aln2.sequences << Sequence.new(rec.id, rec.seq)
  end

Write a (simple) version of pal2nal would be something like

  fasta3 = FastaWriter.new('nt-aln.fa')
  aln.each_with_index do | aaseq, i |
    ntseq = aln2.sequences[i]
    aaseq.id.should == ntseq.id
    codonseq = CodonSequence.new(ntseq.id, ntseq.seq)
    codon_pos = 0
    result = []
    aaseq.each do | aa |
      result <<
        if aa.gap?
          '---'
        else
          codon_pos += 1
          codonseq[codon_pos-1].to_s
        end
    end
    fasta3.write(aaseq.id, result.join(''))
  end

With amino acid aln1 and nucleotide aln2 loaded, the library version is the shorter

  aln3 = aln1.pal2nal(aln2)

aln3 containing the codon alignment.

The API documentation is online. For more code examples see ./spec/.rb and ./features/

Cite

If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475

Copyright

Biogems.info

This exciting Ruby Biogem is published on http://biogems.info/