J. Tarhio and H. Peltola. String matching in the DNA alphabet. Software Practice and Experience, 27(7):851-861, 1997. Home/Search Document Not in Database Summary Related Articles Check |
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Text Searching: Theory and Practice - Baeza-Yates, Navarro (Correct)
....i i d[t i m ] Figure 6: Horspool algorithm with skip loop included. windows by more than 4 positions on average, no matter how large is m. One way to circumvent this weakness is to arti cially enlarge the alphabet. This folklore idea has been reinvented several times, see for example [7, 40, 64]. Say that, instead of considering just the last window character to determine the shift, we read the last q characters (that is, the last window q gram) We preprocess P so that, for each possible q gram, we record its smallest distance to the end of the pattern. Then, we use Horspool as usual. ....
J. Tarhio and H. Peltola. String matching in the DNA alphabet. Software Practice and Experience, 27(7):851-861, 1997.
Boyer-Moore String Matching over Ziv-Lempel Compressed Text - Navarro, Tarhio (2000) (6 citations) Self-citation (Tarhio) (Correct)
.... the simple method is fast enough for reasonably large alphabets, it fails to produce good shifts when the alphabet is small (e.g. DNA) Multicharacter techniques, consisting in shifting by q tuples of characters instead of one character, have been successfully applied to search uncompressed DNA [18]. Those techniques effectively increase the alphabet size and produce longer shifts in exchange for slightly more costly comparisons. We have attempted such an approach for our problem. We select a number q and build the shift tables considering q grams. For instance, for the pattern abcdefg , ....
H. Peltola and J. Tarhio. String matching in the DNA alphabet. Software Practice and Experience, 27(7):851--861, 1997.
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