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The Boyer-Moore-Galil String Searching Strategies Revisited
Based on the Boyer–Moore–Galil approach, a new algorithm is proposed which requires a number of character comparisons bounded by 2n, regardless of the number of occurrences of the pattern in the
Sparse dynamic programming I: linear cost functions
Dynamic programming solutions to a number of different recurrence equations for sequence comparison and for RNA secondary structure prediction are considered, when the weight functions used in the recurrences are taken to be linear.
Boosting textual compression in optimal linear time
A general boosting technique for Textual Data Compression that can turn any memoryless compressor into a compression algorithm that uses the “best possible” contexts, and is very simple and optimal in terms of time.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
BackgroundSimilarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment
Improved string matching with k mismatches
A compact version of the authors' algorithm for string matching with k mismatches, achieving a time performance of 0(mlogm+kn) for general alphabets and of 0 (m+ Kn) for alphabet s whose size is fixed.
Genome‐wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI
It is found that ISWI binds genes near their promoters causing specific alterations in nucleosome positioning at the level of the Transcription Start Site, providing an important insights in understanding ISWI role in higher eukaryote transcriptional regulation.
Dynamic Dictionary Matching
A Generalization of the Suffix Tree to Square Matrices, with Applications
A new data structure is described, the Lsuffix tree, which generalizes McCreight's suffix tree for a string to a square matrix and gives efficient algorithms for the static versions of the following dual problems that arise in low-level image processing and visual databases.
On the Exact Complexity of String Matching: Lower Bounds
This paper provides several lower bounds on the number of character comparisons that any string matching algorithm must perform in the worst case in order to find occurrences of a pattern string in a
Improving table compression with combinatorial optimization
This work devise the first on-line training algorithms for table compression, which can be applied to individual files, not just continuously operating sources; and also a new, off-lineTraining algorithm, based on a link to the asymmetric traveling salesman problem, which improves on prior work by rearranging columns prior to partitions.