Provably sensitive Indexing strategies for biosequence similarity search
Proceedings of the sixth annual international conference on Computational biology
Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences
Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
FLASH: A Fast Look-Up Algorithm for String Homology
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Generalized Swap-with-Parent Schemes for Self-Organizing Sequential Linear Lists
ISAAC '97 Proceedings of the 8th International Symposium on Algorithms and Computation
One-Gapped q-Gram Filtersfor Levenshtein Distance
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Better filtering with gapped q-grams
Fundamenta Informaticae - Special issue on computing patterns in strings
Designing multiple simultaneous seeds for DNA similarity search
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Sensitivity analysis and efficient method for identifying optimal spaced seeds
Journal of Computer and System Sciences
On spaced seeds for similarity search
Discrete Applied Mathematics
Estimating Seed Sensitivity on Homogeneous Alignments
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Optimal spaced seeds for faster approximate string matching
Journal of Computer and System Sciences
Hardness of optimal spaced seed design
Journal of Computer and System Sciences
Lossless filter for multiple repetitions with Hamming distance
Journal of Discrete Algorithms
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
Information Processing Letters
Masking patterns in sequences: A new class of motif discovery with don't cares
Theoretical Computer Science
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Quality of algorithms for sequence comparison
PReMI'11 Proceedings of the 4th international conference on Pattern recognition and machine intelligence
Spaced seeds design using perfect rulers
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
A unifying framework for seed sensitivity and its application to subset seeds
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Seed design framework for mapping SOLiD reads
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
SA-REPC: sequence alignment with regular expression path constraint
LATA'10 Proceedings of the 4th international conference on Language and Automata Theory and Applications
Probabilistic Arithmetic Automata and Their Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for path-constrained sequence alignment
Journal of Discrete Algorithms
Design and analysis of periodic multiple seeds
Theoretical Computer Science
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We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Kärkkäinen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.