Figure 1

A paircomp comparison of the otx gene locus from S. purpuratus (top) with L. variegatus (bottom). We used paircomp to compare all 20 bp subsequences from a 160 kb S. purpuratus BAC with a 62 kb L. variegatus BAC; those 20 bp subsequences with a exact match of 19/20 or 20/20 bases are connected with a red line. Only the 80 kb surrounding the otx gene is shown on the top. Matches to the known S. purpuratus cDNA sequence are shown in red on the top sequence, and TBLASTX matches in L. variegatus to the same cDNA sequence are shown in blue on the bottom sequence. The L. variegatus genomic sequence does not extend to cover the 3' region of the coding sequence. On the top of the view are tabs to switch between the "pair view" (shown) and the "dot plot" view (see Figure 2). On the right side of the view are control buttons that allow the user to change both the color and the threshold at which matches are displayed. The user can also view a closeup of a region by selecting the region on the sequence (e.g. as on the bottom sequence, where a region from 40 kb to 61.6 kb is selected) and then pressing the "View closeup..." button. An example closeup view is shown in Figure 3.