Optimal spaced seeds were developed as a method to increase sensitivity of local alignment programs similar to BLASTN. Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison. We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated geno...

Spaced seeds have been shown to be superior to continuous seeds for efficient and sensitive homology search based on the seedand-extend paradigm. Much the same is true in genome mapping of high-throughput short-read data. However, a highly sensitive search with multiple spaced patterns often requires the use of a great amount of index data. We propose a novel seed-set construction method for ef...

We study the problem of computing optimal spaced seeds for identifying homologous coding DNA sequences in large genomic data sets. We develop two models of DNA sequence alignment in coding regions, and using data sets from human/Drosophila and human/mouse comparisons, we compute optimal spaced seeds using a dynamic programming algorithm. The seeds we identify are more sensitive by far at identi...

We consider the problem of lossless spaced seed design for approximate pattern matching. We show that, using mathematical objects known as perfect rulers, we can derive a family of spaced seeds for matching with up to two errors. We analyze these seeds with respect to the trade-off they offer between seed weight and the minimum length of the pattern to be matched. We prove that for patterns of ...