Fig. 1
From: A performant bridge between fixed-size and variable-size seeding
a) The hierarchies for fixed-size seeding (k-mer seeds and minimizer seeds) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds) as well as the mapping among them. The ovals indicate subset relationships among the different seed sets. l denotes the length of an individual variable-size seed. Alg. 1 (Methods Section) constructs MEMs of size ≥k and ≥w + k − 1 out of k-mer seeds and (w, k)-minimizer seeds, respectively. Alg. 2a (Methods Section) in the methods section extracts SMEMs out of MEMs. Alg. 2b (Methods Section) computes maximal spanning seeds from MEMs (or SMEMs). b) visualizes the query positions and extensions of 11 instances of variable-size seeds. All displayed seeds are MEMs. Additionally, the blue and green seeds are SMEMs. Within the SMEMs, the green seeds are maximal spanning seeds. s4 is a MEM merely, because it is enclosed by s3. s2 is not enclosed by any other seed, but it is covered by longer seeds (s1 and s3). Therefore, s2 is a SMEM, but not a maximal spanning seed. s1 is not enclosed by any other seed and is the longest seed on the positions 0 to 7. Therefore, s1 is a maximal spanning seed