Skip to main content
Fig. 2 | BMC Bioinformatics

Fig. 2

From: A performant bridge between fixed-size and variable-size seeding

Fig. 2

Several aspects of the MEM computation from k-mers. a) In a plane spanned by reference (x-axis) and query (y-axis), overlapping k-mers form MEMs. The yellow, green, red and blue 3-mers form a single long MEM that spans 6‚ÄČnt. The two orange seeds are isolated and have no neighbors for merging. The dashed boxes on the reference represent 3-mer entries in the hash-table without a match on the query. The dashed boxes on the query visualize 3-mers that do not occur in the hash-Table. b) In subfigure i), the MEM s is formed by merging five k-mers (the grey boxes with solid outlines). Subfigure ii) shows the situation of i) for 2-step 3-mers, a subset of 3-mers that contains every second 3-mer merely. The first and last nucleotides of s are not covered by 2-step 3-mers and must be discovered by an additional extension

Back to article page