Superiority and complexity of the spaced seeds
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
On the complexity of the spaced seeds
Journal of Computer and System Sciences
Superiority of Spaced Seeds for Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Amino Acid Classification and Hash Seeds for Homology Search
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
On Subset Seeds for Protein Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
Information Processing Letters
New algorithms for the spaced seeds
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Quality of algorithms for sequence comparison
PReMI'11 Proceedings of the 4th international conference on Pattern recognition and machine intelligence
A unifying framework for seed sensitivity and its application to subset seeds
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Fast computation of good multiple spaced seeds
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
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Biologists highly rely on good algorithms for findinghomologous regions in bimolecular sequences. An advancedhomology search program named PatternHunterhas recently been developed. Unlike the well-known programBLAST using a consecutive model, it utilizes a spacedseed model to attain higher sensitivity. We have developeda new program, which extends PatternHunter from a singlespaced model to a multiple spaced model. In this paper,we describe methods for finding optimal single and multiplespaced models.