A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores

[摘要] Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model computes a P-value assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Using a simple approach combined with recent results in reliability theory, we demonstrate here that the Karlin-Altshul model can be derived with no reference to the extreme events theory.

[学科分类] 生物技术

[关键词] conservation function;reliability theory;Karlin-Altshul theorem