Maximilian Schlosshauer and Mattias Ohlsson A Novel Approach To Local Reliability Of Sequence Alignments Bioinformatics 18, 847-854 (2002) Abstract: Motivation The alignment of biological sequences obtained from an algorithm will in general contain both correct and wrong parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified. Results We present a novel approach that attributes a reliability index to every pair, including gapped regions, in the optimal alignment of two protein sequences. The method is based on a fuzzy recast of the dynamic programming algorithm for sequence alignment in terms of mean field annealing. An extensive evaluation with structural reference alignments not only shows that the probability for a pair to be correctly aligned grows consistently with increasing reliability index, but moreover demonstrates that the value of the reliability index can directly be translated into an estimate of the probability for a correct alignment. LU TP 01-25