STELLAR: Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast but heuristic, and hence often miss significant matches. We provide here the local pairwise aligner STELLAR that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy. STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments in the edit or hamming distance model.
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