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Biosequence Similarity Search on the Mercury System (2004)  (Make Corrections)  (1 citation)
Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Joseph Lancaster



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Abstract: Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports... (Update)

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P. Krishnamurthy, J. Buhler, R. Chamberlain, M. Franklin, K. Gyang, and J. Lancaster, Biosequence similarity search on the mercury system, 15th IEEE Int. Conference on Application-Speci c Systems, Architectures and Processors (ASAP'04), 2004. http://citeseer.ist.psu.edu/krishnamurthy04biosequence.html   More

@misc{ krishnamurthy04biosequence,
  author = "P. Krishnamurthy and J. Buhler and R. Chamberlain and M. Franklin and K.
    Gyang and J. Lancaster",
  title = "Biosequence similarity search on the mercury system",
  text = "P. Krishnamurthy, J. Buhler, R. Chamberlain, M. Franklin, K. Gyang, and
    J. Lancaster, Biosequence similarity search on the mercury system, 15th
    IEEE Int. Conference on Application-Speci c Systems, Architectures and Processors
    (ASAP'04), 2004.",
  year = "2004",
  url = "citeseer.ist.psu.edu/krishnamurthy04biosequence.html" }
Citations (may not include all citations):
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240   Identification of common molecular subsequences - Smith, Waterman - 1981
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25   Searching genetic databases on Splash - Hoang - 1995
15   Multiple filtration and approximate pattern matching (context) - Pevzner, Waterman - 1995
15   Deep packet inspection using parallel bloom filters - Dharmapurikar, Krishnamurthy et al. - 2004
14   Active disks for large-scale data processing - Reidel, Faloutsos et al. - 2001
8   Initial sequencing and comparative analysis of the mouse gen.. (context) - Waterston - 2002
8   Kestrel: a programmable array for sequence analysis - Hirschberg, Hughley et al. - 1996
5   Merrimac: Supercomputing with streams - Dally - 2003
4   A reconfigurable parallel disk system for filtering genomic .. (context) - Lavenier, Guytant et al. - 2003
3   Massively parallel data mining using reconfigurable hardware.. (context) - Zhang - 2004
2   High speed homology search with FPGAs - Yamaguchi, Maruyama et al. - 2002
1   Growth of GenBank (context) - for, Information - 2002
1   An FPGA-based search engine for unstructured database (context) - West - 2003
1   The Mercury system: Exploiting truly fast hardware for data .. - Chamberlain - 2003
1   An architecture for fast processing of large unstructured da.. (context) - Franklin - 2004
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