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Table 7 Alignment based results

From: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

  UPGMA NJ
salign-CK-36-PDB-BLOSUM62-local 0.9849 0.7677
salign-CK-36-PDB-PAM120-global 0.9533 0.8556
salign-SP-86-PDB-BLOSUM62-local 0.5391 0.5481
salign-SP-86-PDB-PAM120-global 0.5488 0.5491
cor-word-1-CK-36-PDB 0.5600 0.5718
cor-word-2-CK-36-PDB 0.5837 0.5837
cor-word-3-CK-36-PDB 0.5117 0.5616
cor-word-1-SP-86-PDB 0.5447 0.5356
cor-word-2-SP-86-PDB 0.5319 0.5265
cor-word-3-SP-86-PDB 0.5392 0.5292
  1. Experimental results for the CK-36-PDB and the SP-86-PDB data sets, with different alternative methods to build distance matrices, that is, global and local alignments as well as k-tuple statistics and correlations. For each distance matrix associated to a method, we report the F-measure for both UPGMA and NJ methods.