Patricia A. Evans

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Molecular biologists use algorithms that compare and otherwise analyze sequences that represent genetic and protein molecules. Most of these algorithms, however, operate on the basic sequence and do not incorporate the additional information that is often known about the molecule and its pieces. This research describes schemes to combinatorially annotate(More)
Discovering patterns in strings is a central task in analyzing molecular sequences. One pattern discovery problem is to find a pattern that occurs as a substring in each member of a given set of strings. Additionally, occurrences of this pattern are allowed to have up to some specified number of errors, so the occurrences may not exactly match the pattern.(More)
Problems associated with ÿnding strings that are within a speciÿed Hamming distance of a given set of strings occur in several disciplines. In this paper, we use techniques from pa-rameterized complexity to assess non-polynomial time algorithmic options and complexity for the COMMON APPROXIMATE SUBSTRING (CAS) problem. Our analyses indicate under which(More)