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Motivation: Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive auto-matic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annota-tion or multiple-genomic tree constructions. Extreme value dis-tribution based on the Karlin–Altschul model, usually advised for large-scale comparisons are not always valid, particularly in the case of comparisons of non-biased with nucleotide-biased genomes (such that of Plasmodium falciparum). Z-values estimates based on Monte Carlo technics, can be calculated experimentally for any alignment output, whatever the method used. Empirically, a Z-value higher than ∼8 is supposed reas-
O. Bastien (Thu,) studied this question.