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Table 2 Motif characteristics affecting quality of motif alignment.

From: A new protein linear motif benchmark for multiple sequence alignment software

 

clustalw

dialign

kalign

mafft_linsi

mummals

muscle

probcons

tcoffee

context

0.4601

0.5314

0.5686

0.6983

0.6030

0.6672

0.5528

0.6159

conservation

0.1557

0.0848

-0.0070

0.0729

0.0707

-0.0037

0.0513

0.0370

length

0.1298

0.1857

0.0274

0.0147

0.0923

0.0324

0.0083

0.0339

  1. Pearson correlation coefficients for SPS scores versus structural, motif conservation and motif length, for the eight different alignment programs evaluated. Values in bold indicate a significant correlation (critical value = 0.306 for 95% confidence interval)