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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

Statistics

   

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.
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BMC Bioinformatics

ISSN: 1471-2105

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