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Table 3 Average CPU time* required to calculate one structure alignment of ten different algorithms

From: MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments

Algorithm

MALIDUP-sq

MALIDUP-ns

MALISAM-sq

MALISAM-ns

DaliLite

0.910s

1.019s

0.445s

0.539s

TM-align

0.111s

0.087s

0.055s

0.043s

CE

0.152s

—

0.055s

—

MICAN

0.134s

0.134s

0.098s

0.097s

DEDAL

5.734s

6.000s

0.272s

0.259s

SNAP

1.517s

1.743s

0.962s

1.128s

GANGSTA+

0.270s

0.273s

0.185s

0.190s

SCALI

8.272s

8.153s

2.723s

2.870s

MASS

0.138s

0.136s

0.105s

0.106s

SAMO

0.454s

0.455s

0.166s

0.163s

  1. *CPU times are measured on a PC with Intel Core-i7 2.93 GHz processor.
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BMC Bioinformatics

ISSN: 1471-2105

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