Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length

Rasmussen KR, Stoye J, Myers EW (2005)
In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 189-203.

Conference Paper | Published | English

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Abstract
Fast and exact comparison of large genomic sequences remains a challenging task in biosequence analysis. We consider the problem of finding all c-matches between two sequences, i.e. all local alignments over a given length with an error rate of at most E. We study this problem theoretically, giving an efficient q-gram filter for solving it. Two applications of the filter are also discussed, in particular genomic sequence assembly and BLAST-like sequence comparison. Our results show that the method is 25 times faster than BLAST, while not being heuristic.
Publishing Year
Conference
RECOMB 2005
Location
Cambridge, MA, USA
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Rasmussen KR, Stoye J, Myers EW. Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. In: Proc. of RECOMB 2005. LNBI. Vol 3500. SPRINGER-VERLAG BERLIN; 2005: 189-203.
Rasmussen, K. R., Stoye, J., & Myers, E. W. (2005). Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. Proc. of RECOMB 2005, 3500, 189-203.
Rasmussen, K. R., Stoye, J., and Myers, E. W. (2005). “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length” in Proc. of RECOMB 2005 LNBI, vol. 3500, (SPRINGER-VERLAG BERLIN), 189-203.
Rasmussen, K.R., Stoye, J., & Myers, E.W., 2005. Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. In Proc. of RECOMB 2005. LNBI. no.3500 SPRINGER-VERLAG BERLIN, pp. 189-203.
K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.189-203.
Rasmussen, K.R., Stoye, J., Myers, E.W.: Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length. Proc. of RECOMB 2005. LNBI. 3500, p. 189-203. SPRINGER-VERLAG BERLIN (2005).
Rasmussen, Kim R., Stoye, Jens, and Myers, Eugene W. “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”. Proc. of RECOMB 2005. SPRINGER-VERLAG BERLIN, 2005.Vol. 3500. LNBI. 189-203.
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