A shortest path between two nodes, i and j, is a minimal length path between them.
To identify matching sequences, Vmatch first computes all maximal exact matches of a given minimal length (seeds) between all sequences.
In this study we show that the minimal chromosomal space is required for transcriptional regulation in yeast species; while the minimal length varies between yeast species, this variation is relatively small.
The minimal length of discrimination between sequences of reference strains is for the V1 region described in Fig. 2. Positions refers to E. coli numbering[ 11].
The distance d v, w) between two nodes v, w is defined as the minimal length of any path between them.
Interestingly, while the minimal length does not vary between age groups, the relative weight of the two peaks for divergent regions shifts from longer regions to short regions with increasing age.
We estimate the length of the gene conversion tract by averaging the maximal length of the tract (the distance between markers that are not within the gene conversion tract: 8.8 kb) and the minimal length of the tract (the distance between the converted markers: 3.5 kb).
Consistent with Figure 1, the minimal length appears to be very similar between uni-directional and divergent regions in each age class.
Based on their affinities to Spy (Kd = 2.5, 2.3, 2.6, and 8 µM for the full length Im7 L53 4554A, 3–45, 7 45, and 12 45 peptide, respectively) and their expression levels, we chose the 7 45 fragment as the minimal length peptide that represents the interaction between Spy and Im7 L53A Im7A.
This minimal length ensured a minimum of 5% overlap between Pachycladon homeologues.
