Numerical recipes in C (2nd ed.): the art of scientific computing
Numerical recipes in C (2nd ed.): the art of scientific computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
LATIN '98 Proceedings of the Third Latin American Symposium on Theoretical Informatics
Proceedings of the sixth annual international conference on Computational biology
Database indexing for large DNA and protein sequence collections
The VLDB Journal — The International Journal on Very Large Data Bases
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
Assessing the Statistical Significance of Overrepresented Oligonucleotides
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Extracting Common Motifs under the Levenshtein Measure: Theory and Experimentation
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Using Suffix Trees for Gapped Motif Discovery
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Finding Higher Order Motifs under the Levenshtein Measure
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Cooperative Metaheuristics for Exploring Proteomic Data
Artificial Intelligence Review
On the complexity of finding common approximate substrings
Theoretical Computer Science
Fast and Practical Algorithms for Planted (l, d) Motif Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Suffix tree characterization of maximal motifs in biological sequences
Theoretical Computer Science
Extracting approximate patterns
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
An Improved Heuristic Algorithm for Finding Motif Signals in DNA Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Removing artifacts of approximated motifs
ITBAM'11 Proceedings of the Second international conference on Information technology in bio- and medical informatics
Accelerating motif discovery: motif matching on parallel hardware
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
On-Line linear-time construction of word suffix trees
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Computing exact p-value for structured motif
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Characterization and extraction of irredundant tandem motifs
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
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This paper introduces two exact algorithms for extracting conserved structured motifs from a set of DNA sequences. Structured motifs are composed of p ⪈ 2 parts separated by constrained spacers These algorithms use a suffix tree for fulfilling this task. They are efficient enough to be able to extract site consensus, such as promoter sequences, from a whole collection of non coding sequences extracted from a genome. In particular, their time complexity scales linearly with N2n where n is the average length of the sequences and N their number. An application with interesting results to the identification of promoter consensus sequences in bacterial genomes is shown.