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Table 1 Correlation coefficients of the translation dependent scores used on non-frameshifted amino acids, with BLOSUM scores and classic DNA scores

From: Back-translation for discovering distant protein homologies in the presence of frameshift mutations

 

DNA

BLOSUM 62

TDS M (0.1)

0.86

0.52

TDS M (0.3)

0.81

0.50

TDS M (0.5)

0.77

0.50

TDS M (0.7)

0.75

0.50

TDS M (1.0)

0.71

0.47

TDS E

0.59

0.88

  1. The correlation coefficients between several types of scores that can be used to align amino acids without a frameshift: i) expected amino acid pair scores obtained from codon alignment with a classic match/mismatch scoring scheme (denoted DNA); ii) expected amino acid pair scores obtained from the translation-dependent scoring matrices based on the mechanistic codon substitution model (denoted TDS M ); iii) expected amino acid pair scores obtained from the translation-dependent scoring matrices based on the empirical codon substitution model (denoted TDS E ); iv) BLOSUM matrices for amino acid sequence alignment.
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Algorithms for Molecular Biology

ISSN: 1748-7188