Source | Length, Mbp | Time, min g= 3 | Time, min g= 0 | Longest period |
|---|
S. cerevisiae Chr. I | 0.23 | 0.25 | 0.12 | 135 (17.9) |
S. cerevisiae Chr. VIII | 0.56 | 0.58 | 0.29 | 1998 (2) |
H. sapiens β TCR | 0.68 | 0.77 | 0.36 | 340 (2) |
S. cerevisiae Chr. XII | 1.0 | 1.2 | 0.49 | 9137 (2) |
M. magneticum AMB-1 | 4.9 | 6.4 | 2.2 | 1158 (4.2) |
H. sapiens Chr. I contig | 9.8 | 13.5 | 4.7 | 18557 (2.1) |
Source
|
Length, Mbp
|
Time, min
g
= 3
|
Time, min
g
= 0
|
Longest period
|
H. sapiens Chr. XXI | 33.0 | 34.4 | 16.4 | 3379 (2) |
R. norvegicus
| 80.7 | 86.7 | 39.1 | 2715 (2) |
H. sapiens Chr. X | 127.6 | 134.7 | 64.1 | 4863 (2) |
M. musculus Chr I | 202.5 | 239.1 | 90.0 | 3773 (2) |
Source
|
No. of Proteins
|
Time, min
g
= 3
|
Time, min
g
= 0
|
# TRs (# TRPs)
|
Swiss-Prot v.30 | 40292 | 1.5 | 0.55 | 2428 (3771) |
Swiss-Prot v.38 | 80000 | 2.6 | 1.1 | 3762 (7012) |
Swiss-Prot v.45 | 163633 | 5.4 | 2.4 | 5302 (12359) |
Swiss-Prot v.50.5 | 230150 | 7.3 | 3.5 | 6444 (17097) |
- Running times for the analysis of different input sequence datasets are shown, with the gap parameter g = 3, or g = 0. The following DNA sequences were downloaded from NCBI: S. cerevisiae Chromosomes I (gi 85666109), VIII (gi 82795252), and XII (gi 85666119), H. sapiens Chromosomes X (gi 89033689) and XXI (89058287), Chromosome I contig (gi 29789880), and the β T-cell receptor locus (gi 114841177), R. norvegicus Chromosome XVI (gi 109504251), M. musculus Chromosome I (gi 83274080), and the M. magneticum AMB-1 (gi 82943940) genome. Sequences at the top (0.23 – 9.8 Mbp) were run with minD = 20, minP = 1, and all possible maximum periods. Longer DNA sequences (33 – 202.5 Mbp) were run with minD = 50, minP = 10, and (due to memory limitations) maximum period = 100 kbp; divide-and-conquer (see Appendix) was used for periods < 1000 (fragment length = 1 Mbp). For each longest period found, the copy number is shown in parentheses. These data show a linear relationship between running time and increasing input sequence length (R2 > 0.99). Running times for analysis of 4 Swiss-Prot datasets, using minD = 10 and minP = 1, shown at the bottom, including the number of TRs detected (using consensus comparison, see Appendix) and the number of TR-containing proteins found (in parentheses). XSTREAM running time scaled linearly with increasing Swiss-Prot dataset size (R2 > 0.998).
