The Genomes of Oryza sativa: A History of Duplications (original) (raw)
Figure 1
Basic Algorithm for Construction of Scaffolds and Super-Scaffolds
We start with the smallest plasmids and progressively work our way up to the largest BACs. Only links with two or more pieces of supporting evidence are made. These include 34,190 “anchor points” constructed from a comparison of indica and japonica. Each anchor is a series of high-quality BlastN hits (typically 98.5% identity) put together by a dynamic programming algorithm that allows for small gaps to accommodate the polymorphic intergenic repeats. Typical anchor points contain four BlastN hits at a total size of 9 kb (including gaps). Notice how in the beginning indica and japonica are processed separately, to construct what we called scaffolds. Only at the end do we use data from one subspecies to link scaffolds in the other subspecies, and these are what we called super-scaffolds.