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Amino Acid Classification and Hash Seeds for Homology Search
- BICOB
, 2009
"... 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
Abstract
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Cited by 2 (1 self)
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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.

