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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