Table 1 Algorithm performance comparing biologically related sequences of similar length
From: Improved algorithms for approximate string matching (extended abstract)
Sequence A | Sequence B | Alphabet size | (Average) length | Our algorithm (sec) | Ukkonen's algorithm (sec) | Basic algorithm (sec) | (Average) edit distance |
|---|---|---|---|---|---|---|---|
Random 16S rRNA sequence | Random 16S rRNA sequence | 4 | 1350 | 0.679 | 0.811 | 2.554 | 421.3 |
Hyphomonas 16S rRNA (AF082798) | Hyphomonas 16S rRNA (AF082795) | 4 | 1330 | 0.25 | 0.18 | 2.14 | 46 |
Alphaproteobacteria 16S rRNA (AJ238567) | Betaproteobacteria 16S rRNA (AJ239278) | 4 | 1320 | 0.42 | 0.46 | 2.07 | 318 |
Cucumber necrosis virus genome | Lisianthus necrosis virus genome | 4 | 4790 | 6.70 | 6.32 | 28.27 | 1154 |
Human poliovirus 1 virion protein | Human Rhinovirus A virion protein | 20 | 870 | 1.02 | 1.05 | 0.88 | 472 |