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.

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Konferenzbeitrag | Veröffentlicht | Englisch
Autor
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Abstract / Bemerkung
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.
Erscheinungsjahr
Titel des Konferenzbandes
Proc. of RECOMB 2005
Band
3500
Seite
189-203
Konferenz
RECOMB 2005
Konferenzort
Cambridge, MA, USA
ISSN
PUB-ID

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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, LNBI, 3500, 189-203. SPRINGER-VERLAG BERLIN. doi:10.1007/11415770_15
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.