Combinatorial Pattern Matching: ... Annual SymposiumSpringer-Verlag, 2005 - Combinatorial analysis |
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Page 46
... space , while the text takes n logo bits1 . In practice the suffix tree requires about 20 times the text size . A smaller constant factor , close to 4 in practice , is achieved by the suffix array [ 16 ] . Yet , the space complexity is ...
... space , while the text takes n logo bits1 . In practice the suffix tree requires about 20 times the text size . A smaller constant factor , close to 4 in practice , is achieved by the suffix array [ 16 ] . Yet , the space complexity is ...
Page 54
... space ) , we see that self - indexes are considerably fast for counting , especially for short patterns . For longer ones , their small space consumption is paid in a 10X slowdown for counting . Yet , this is orders of magnitude faster ...
... space ) , we see that self - indexes are considerably fast for counting , especially for short patterns . For longer ones , their small space consumption is paid in a 10X slowdown for counting . Yet , this is orders of magnitude faster ...
Page 57
... space , which is the fastest algorithm using O ( n log || ) -bit working space . In this paper we give an efficient algorithm to construct the index data structures for large alphabets . Our algorithm constructs the suffix array , the ...
... space , which is the fastest algorithm using O ( n log || ) -bit working space . In this paper we give an efficient algorithm to construct the index data structures for large alphabets . Our algorithm constructs the suffix array , the ...
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