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We present a novel approach to managing redundancy in sequence databanks such as GenBank. We store clusters of near-identical sequences as a representative union-sequence and a set of corresponding edits to that sequence. During search, the query is compared to only the union-sequences representing each cluster; cluster members are then only reconstructed(More)
Homology search is a key tool for understanding the role, structure, and biochemical function of genomic sequences. The most popular technique for rapid homology search is blast, which has been in widespread use within universities, research centers, and commercial enterprises since the early 1990s. In this paper, we propose a new step in the blast(More)
BLAST is the most popular bioinformatics tool and is used to run millions of queries each day. However, evaluating such queries is slow, taking typically minutes on modern workstations. Therefore, continuing evolution of BLAST--by improving its algorithms and optimizations--is essential to improve search times in the face of exponentially increasing(More)
After pilocarpine-induced status epilepticus, many granule cells born into the postseizure environment migrate aberrantly into the dentate hilus. Hilar ectopic granule cells (HEGCs) are hyperexcitable and may therefore increase circuit excitability. This study determined the distribution of their axons and dendrites. HEGCs and normotopic granule cells were(More)
Molecular biologists, geneticists, and other life scientists use the BLAST homology search package as their first step for discovery of information about unknown or poorly annotated genomic sequences. There are two main variants of BLAST: BLASTP for searching protein collections and BLASTN for nucleotide collections. Surprisingly, BLASTN has had very little(More)
We present a new approach to managing redundancy in sequence databanks such as GenBank. We store clusters of near-identical sequences as a representative union-sequence and a set of corresponding edits to that sequence. During search, the query is compared to only the union-sequences representing each cluster; cluster members are then only reconstructed and(More)
Detection of highly similar sequences within genomic collections has a number of applications, including the assembly of expressed sequence tag data, genome comparison, and clustering sequence collections for improved search speed and accuracy. While several approaches exist for this task, they are becoming infeasible — either in space or in time — as(More)
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