Combinatorial Pattern Matching: ... Annual SymposiumSpringer-Verlag, 2005 - Combinatorial analysis |
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Page 77
... running time for Step 1 is O ( m log m ) . The running time for Step 2 is 4b0 ( m logm ) , since 4b FFTs have to be calculated . The running time for Step 3 is O ( m2 / b ) , so the total time is O ( m2 / b + 4bm log m ) . Taking b = m ...
... running time for Step 1 is O ( m log m ) . The running time for Step 2 is 4b0 ( m logm ) , since 4b FFTs have to be calculated . The running time for Step 3 is O ( m2 / b ) , so the total time is O ( m2 / b + 4bm log m ) . Taking b = m ...
Page 88
... running time . The results show a clear tendency that , as x increases from one to seven , FAAST can shift by larger distances on average and make fewer comparisons . Though the preprocessing time is increasing , the total running time ...
... running time . The results show a clear tendency that , as x increases from one to seven , FAAST can shift by larger distances on average and make fewer comparisons . Though the preprocessing time is increasing , the total running time ...
Page 89
... running time of the Tarhio - Ukkonen algorithm with our generalized algorithm FAAST . This was repeated 5 times and the average result was reported . The bacterial sequence set includes totally 170K bases and the fungal sequence set ...
... running time of the Tarhio - Ukkonen algorithm with our generalized algorithm FAAST . This was repeated 5 times and the average result was reported . The bacterial sequence set includes totally 170K bases and the fungal sequence set ...
Contents
Sharper Upper and Lower Bounds for an Approximation Scheme | 1 |
Text Indexing with Errors | 21 |
Succinct Suffix Arrays Based on RunLength Encoding | 45 |
Copyright | |
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Common terms and phrases
algorithm alignment alphabet Apostolico approximate automaton Bioinformatics bits bound breakpoint Burrows-Wheeler transform c-token character column complexity Computer Science consensus PQ tree consider constraints construction Corasick corresponding Crochemore data structure defined Definition denote DFTDP DIST DNA sequences dynamic programming edges edit distance efficient encoding errors example exons function gene genome given graph Hamming distance implementation input integer interval label Lemma length linear LNCS mass matching problem Max-SNP maximal median minimal consensus PQ mismatches motif multiset node O(n log obtained occurrences optimal output p₁ pair Parsing path pattern matching peak permutations polynomial position PQ tree prefix prefix-free preprocessing Proc Proof protein regular expression rigid subsequence S₁ score Section shift distance space spin images Springer-Verlag string matching substring suffix array suffix tree term tree Theorem trie variable vector vertex WDWG words