Now here is the exciting part! You can see that the scoring algorithms work reasonably well to predict clusters that should be linked. Oftentimes, there is clearly one link that has a score superior to all the others, and deciding that it should be confirmed is easy. RunAbout now allows you to quickly assign all this “low-hanging fruit” automatically with a single button: “Extend” (located at the bottom of the window under the Fragments display):
Clicking the Extend button will instantly link all the highest-scoring clusters that are consecutively linked to the cluster you’re currently examining. Three criteria must be met for the assignments to be extended: 1) the score for the match must be > 2.2, 2) three carbon frequencies must match (thus, links with glycines must all be manually confirmed), and 3) the link must be classified as RAV. These criteria can be changed in the Parameters tab. To illustrate, here is what happens to the data shown above when the Extend button is clicked:
You can see right away that the series of linked clusters “9-0-77” is instantaneously extended to “46-49-24-14-25-9-0-77”. Wow! RunAbout also suggests that this segment corresponds to the amino acid residue sequence “DQQRLIFAG”, as indicated in both the “Match Scores” and “Sequence” panels. “Extend” operates in both directions, but here it was stopped in the C-terminal direction because it encountered a potential glycine residue, which “Extend” does not link to automatically. In the N-terminal direction, Extend stopped at D39 because there is no cluster in that direction that scores high enough for cluster 46 to link to. Extend only works with links that score high enough that they would be pretty obvious anyway; it is thus more of a time-saving device than a mystery solver.