Section: New Results

Minimal absent words

Minimal absent words are words that do not occur but whose proper factors all occur in the sequence. In a collaboration with King's College, several algorithms, we have designed algorithms to search for minimal absent words in external memory [8], and in-line, using a sliding window [13] (parallelization, external memory,...) that outperform previous solutions and achieve near-optimal speed up. This opens new scenarios in the applications of minimal absent words in computational biology, including phylogeny or evolution. For instance, it was shown that there exist three minimal words in Ebola virus genomes which are absent from human genome. As two strings coincide iff they have the same set of minimal absent words, an interesting side result is to solve in optimal time the pattern matching problem using negative information.