Table 1 Run time (mm:ss) of the Perl and C++ programs compared to MoSDi (exact and approximated using compound Poisson) for calculating the occurrence distribution for s motif query sequences of length m (13–31) over a reference genome of 5 million bases
From: Fast and exact quantification of motif occurrences in biological sequences
No. of motifs s | Motif length m | C++ | Perl | MoSDi exact (10/500) | MoSDi approx (10/500) |
|---|---|---|---|---|---|
10 | 13 | 00:00 | 00:00 | 00:47/17:50 | 00:00/00:00 |
20,000 | 13 | 00:01 | 00:07 | xx:xx/xx:xx | 01:16/02:24 |
50,000 | 13 | 00:03 | 00:18 | xx:xx/xx:xx | 03:14/06:24 |
200,000 | 13 | 00:15 | 01:12 | xx:xx/xx:xx | 13:34/27:40 |
400,000 | 13 | 00:35 | 02:20 | xx:xx/xx:xx | 28:05/xx:xx |
1,000,000 | 13 | 00:85 | 05:45 | xx:xx/xx:xx | xx:xx/xx:xx |
10 | 31 | 00:00 | 00:00 | 01:47/xx:xx | 00:00/00:01 |
20,000 | 31 | 00:02 | 00:07 | xx:xx/xx:xx | 15:34/16:41 |
50,000 | 31 | 00:04 | 00:17 | xx:xx/xx:xx | xx:xx/xx:xx |
200,000 | 31 | 00:16 | 01:09 | xx:xx/xx:xx | xx:xx/xx:xx |
400,000 | 31 | 00:29 | 02:26 | xx:xx/xx:xx | xx:xx/xx:xx |
1,000,000 | 31 | 00:32 | 05:18 | xx:xx/xx:xx | xx:xx/xx:xx |