Alignment Cylinder. A genomic sequence from Human Y chromosome in the nucleotide view (A) is shown alongside a hypothetical 3D cylindrical architecture (B). The example sequence is human alpha satellite that is interrupted by a few pieces of non-alignable DNA. The primary repeat has a circumference of 171 bp and tiny variations in the cylinder's diameter negate most of the indels so that the repeat aligns vertically. This creates a continuous alignment in 3D space without the introduction of any gaps or other artificial constructs. The areas of non-alignable DNA are represented by loose, unorganized loops since they have no obvious preferred position.
Seaman and Sanford BMC Bioinformatics 2009 10:452 doi:10.1186/1471-2105-10-452