Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Simple and flexible detection of contiguous repeats using a suffix tree
Theoretical Computer Science
Computation of Squares in a String (Preliminary Version)
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
DNA Sequence Compression Using the Burrows-Wheeler Transform
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Finding Maximal Repetitions in a Word in Linear Time
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Searching BWT Compressed Text with the Boyer-Moore Algorithm and Binary Search
DCC '02 Proceedings of the Data Compression Conference
The SCP and Compressed Domain Analysis of Biological Sequences
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Computing all repeats using suffix arrays
Journal of Automata, Languages and Combinatorics - Special issue: Selected papers of the 13th Australasian workshop on combinatorial algorithms
Variations of the parameterized longest previous factor
Journal of Discrete Algorithms
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We present a new data structure called the BSCP (block sorted common prefix), and its tree representation, called the BSCP tree. We also introduce the notion of PTR family 驴 a biologically motivated description and representation of the tandem repetitions in a sequence. The PTR family implicitly encodes each distinct primitive tandem repeat in the sequence as its part. Based on the BSCP tree, we describe a method to locate all the primitive tandem repeat families in an input sequence T. The proposed method requires average space and time complexity in O(u), where u = |T|.