Skip to main content


Fig. 5 | Algorithms for Molecular Biology

Fig. 5

From: Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays

Fig. 5

Timing results for variants of enhanced suffix arrays. The graph shows times in ms per query for the genomes tested: fly (dm5), chicken (gg4), and human (hg19). Within each genome, methods tested are: integer vector representations of the LCP and child arrays (ESA); bytecoding of both arrays (Byte); bytecoding with exception guide arrays at intervals of 1024 (Guide); addition of a discriminating character array (DC); and using an integrated data structure that combines the LCP, child, and DC arrays (GDI). For each method, timing is measured for 12-, 24-, and 36-nucleotide patterns

Back to article page