Table 5 Execution time (in seconds) of the Nussinov RNA folding codes for 32 threads and different lengths of RNA strands. mRNAs acquired from the NCBI database
From: Tuning iteration space slicing based tiled multi-core code implementing Nussinov’s RNA folding
mRNA definition | Lenght | Serial time | Chang | Li | PluTo [ 8×8×1] | ISS [ 2×6×300] | ISS [ 1×96×8] |
|---|---|---|---|---|---|---|---|
MAPK1, trans. var. 1 | 5916 | 606,32 | 31,05 | 14,95 | 25,94 | 19,52 | 12,92 |
MAPK1, trans. var 2 | 1514 | 2,30 | 0,25 | 0,21 | 0,16 | 0,14 | 0,32 |
MAP2K5, trans. var 2 | 2355 | 15,57 | 0,92 | 0,48 | 0,82 | 0,51 | 0,72 |
MAP2K7, trans. var. 1 | 3525 | 102,32 | 4,46 | 2,74 | 3,51 | 2,63 | 2,53 |
MAP2K6, trans. var. 2 | 13577 | 6127,09 | 437,60 | 168,25 | 347,78 | 257,00 | 152,54 |
MAP3K2 | 10870 | 3033,73 | 229,53 | 86,30 | 171,54 | 121,44 | 70,68 |
MAP4K3, trans. var 1 | 4362 | 221,82 | 10,07 | 6,06 | 8,19 | 6,46 | 5,21 |
MAP4K4, trans. var. 4 | 7183 | 926,43 | 54,43 | 25,65 | 47,40 | 32,67 | 21,45 |