Research Article
A Protein Sequence Analysis Hardware Accelerator Based on Divergences
Table 6
Second-stage performance estimations.
| Sequence set elements | Number of HMM nodes | Entire sequence set processing time in unaccelerated HMMER (sec) | Significant sequences reprocessing time with prefilter and unaccelerated HMMER (sec) | Divergence accelerated significant sequences reprocessing time (sec) |
| 687406 | 788 | 23.40 | 0.234 | 0.0515 | 10 | 0.40 | 0.004 | 0.0009 | 226 | 6.55 | 0.0655 | 0.0144 | 337 | 9.85 | 0.0985 | 0.0217 | 2295 | 74.49 | 0.7449 | 0.1639 | 901 | 26.32 | 0.2632 | 0.0579 |
| 697407 | 788 | 24.34 | 0.2434 | 0.0535 | 10 | 0.47 | 0.0047 | 0.001 | 226 | 6.68 | 0.0668 | 0.0147 | 337 | 9.88 | 0.0988 | 0.0217 | 2295 | 78.87 | 0.7887 | 0.1735 | 901 | 27.55 | 0.2755 | 0.0606 |
| 700218 | 788 | 24.40 | 0.244 | 0.0537 | 10 | 0.42 | 0.0042 | 0.0009 | 226 | 6.76 | 0.0676 | 0.0149 | 337 | 10.26 | 0.1026 | 0.0226 | 2295 | 81.23 | 0.8123 | 0.1787 | 901 | 27.41 | 0.2741 | 0.0603 |
| 712734 | 788 | 25.42 | 0.2542 | 0.0559 | 10 | 0.42 | 0.0042 | 0.0009 | 226 | 6.82 | 0.0682 | 0.015 | 337 | 10.09 | 0.1009 | 0.0222 | 2295 | 81.07 | 0.8107 | 0.1784 | 901 | 27.46 | 0.2746 | 0.0604 |
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