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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)
We present algorithms that reduce the time and space needed to solve problems of finding all motifs common to a set of sequences. In particular, we give algorithms that (1) require time and space linear in the size of the input, (2) succinctly encode the output so that the time and space requirements depend on the number of motifs, not directly on motif(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)
Secretin, a gastrointestinal (GI) hormone, was reported in a preliminary study to improve language and behavior in children with autism/pervasive developmental disorder (PDD) and chronic diarrhea. To determine the efficacy of secretin, we completed a double-blind, placebo-controlled, crossover (3 weeks) study in children with autism/PDD and various GI(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)