Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
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
Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Vector seeds: An extension to spaced seeds
Journal of Computer and System Sciences - Special issue on bioinformatics II
Good spaced seeds for homology search
Bioinformatics
Superiority and complexity of the spaced seeds
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
Rapid Homology Search with Neighbor Seeds
Algorithmica
ZOOM! Zillions of oligos mapped
Bioinformatics
Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Hardness of optimal spaced seed design
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Fast computation of good multiple spaced seeds
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
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Spaced seeds have been extensively studied in the homology search field. A spaced seed can be regarded as a very special type of hash function on k -mers, where two k -mers have the same hash value if and only if they are identical at the w (w k ) positions designated by the seed. Spaced seeds substantially increased the homology search sensitivity. It is then a natural question to ask whether there is a better hash function (called hash seed ) that provides better sensitivity than the spaced seed. We study this question in the paper. We propose a strategy to classify amino acids, which leads to a better hash seed. Our results raise a new question about how to design the best hash seed.