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Table 1 Alignment statistics of the homologous Transcription initiation factor IIA (TFIIA) gamma chain sequences from Plasmodium falciparum and Arabidopsis thaliana.

From: Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

Alignment method Blastp Smith-Waterman
Substitution matrix BLOSUM62 BLOSUM62 DirAtPf100
P-value (Karlin-Altschul) 0.008 NA NA
Z-value (Pearson-Lipman) 10 11 12
T-value (TULIP theorem) 0.01 8.10-3 7.10-3
P-value (this work) 1.5.10-6 3.7.10-7 1.10-7
  1. TFIIA gamma sequences from Plasmodium (UniProtKB Q8I4S7_PLAF7) and Arabidopsis (UniProtKB T2AG_ARATH) were aligned with Blastp and Smith-Waterman methods. Statistics were computed following the Karlin-Altschul model (as implemented in the Blastp algorithm) or the Lipman-Pearson Z-value model. The upper bound for the P-value based on the TULIP theorem is given following the formula: T-value = 1/Z-value2. The P-value deduced from the Z-value Gumbel distribution was computed following the model presented here. Substitution matrices were either BLOSUM62, or the asymmetric DirAtPf100 matrix specified for Plasmodium vs. Arabidopsis comparisons. NA: not applicable.