Fig. 5

Behaviour of the algorithm with different M values. Here, as an example, I use the annotation of multiple-residue LPSs in the protein RNQ1_YEAST (Rnq1p, which underlies the [RNQ+]/[PIN+] prion in S. cerevisiae [19]). fLPS has been run with different maximum window size (M) values, and with other parameters set to defaults. With a sufficiently large M (≥80), one large LPS is annotated with signature {QNSG}. For smaller M values, this LPS is broken into smaller LPSs, as depicted by the boxes at the bottom of the figure. The endpoints of LPSs are numbered at the ends of a box. At the top of the figure, the LPS (for M ≥ 80) is highlighted in orange within the RNQ1_YEAST sequence. The endpoints of LPSs for different M values are labelled above the orange text, with the first numeral of the residue position aligned to the position in the sequence