Table 9.
Calculation time and memory size of dynamic programming for sequences of different length
| Sequence | Length (nt) | O(N4) | O(N3) | ||||
|---|---|---|---|---|---|---|---|
| Time (h:min:s) | Memory (MB) | Time (h:min:s) | Memory (MB) | ||||
| E.coli arginine tRNA | 77 | 00:00:00.3 | (00:00:00.3) | 13 | 00:00:00.2 | (00:00:00.3) | 13 |
| Bacillus stearo thermophilus SRP | 268 | 00:00:21 | (00:00:03) | 13 | 00:00:04 | (00:00:03) | 14 |
| Tetrahymena thermophila group I intron | 433 | 00:02:27 | (00:00:12) | 15 | 00:00:14 | (00:00:11) | 16 |
| S.cerevisiae A5 group II intron | 631 | 00:11:59 | (00:00:35) | 16 | 00:00:46 | (00:00:34) | 19 |
| E.coli small subunit rRNA | 1542 | 06:09:03 | (00:06:47) | 31 | 00:13:42 | (00:07:41) | 45 |
| E.coli large subunit rRNA | 2904 | 67:00:43 | (00:47:00) | 73 | 01:41:00 | (01:03:54) | 121 |
Calculation size and time on a computer with Pentium 4, 3.2 GHz, processor and 1 GB of RAM using the gcc (version 3.2.3) compiler on Red Hat Enterprise Linux 3. The algorithm was improved from O(N4) to O(N3) in time complexity. In parentheses are the results with a limitation of internal loop size set at fewer than or equal to 30 unpaired nucleotides. The O(N3) algorithm is the implementation of the Lyngsø et al. (71) algorithm.