Suboptimal Local Alignments across Multiple Scoring Schemes

Michael M, Dieterich C, Stoye J (2004)
In: Proc. of WABI 2004. LNBI, 3240. SPRINGER-VERLAG BERLIN: 99-110.

Konferenzbeitrag | Veröffentlicht | Englisch
 
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Autor/in
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Abstract / Bemerkung
Sequence alignment algorithms have a long standing tradition in bioinformatics. In this paper, we formulate an extension to existing local alignment algorithms: local alignments across multiple scoring functions. For this purpose, we use the Waterman-Eggert algorithm for suboptimal local alignments as template and introduce two new features therein: 1) an alignment of two strings over a set of score functions and 2) a switch cost function 5 for penalizing jumps into a different scoring scheme within an alignment. Phylogenetic footprinting, as one potential application of this algorithm, was studied in greater detail. In this context, the right evolutionary distance and thus the scoring scheme is often not known a priori. We measured sensitivity and specificity on a test set of 21 human-rodent promoter pairs. Ultimately, we could attain a 4.5-fold enrichment of verified binding sites in our alignments.
Stichworte
footprinting; sequence alignment; non-parametric alignment; comparative sequence analysis; phylogenetic
Erscheinungsjahr
2004
Titel des Konferenzbandes
Proc. of WABI 2004
Band
3240
Seite(n)
99-110
Konferenz
WABI 2004
Konferenzort
Bergen, Norway
ISSN
0302-9743
Page URI
https://pub.uni-bielefeld.de/record/1606286

Zitieren

Michael M, Dieterich C, Stoye J. Suboptimal Local Alignments across Multiple Scoring Schemes. In: Proc. of WABI 2004. LNBI. Vol 3240. SPRINGER-VERLAG BERLIN; 2004: 99-110.
Michael, M., Dieterich, C., & Stoye, J. (2004). Suboptimal Local Alignments across Multiple Scoring Schemes. Proc. of WABI 2004, LNBI, 3240, 99-110. SPRINGER-VERLAG BERLIN. doi:10.1007/978-3-540-30219-3_9
Michael, M., Dieterich, C., and Stoye, J. (2004). “Suboptimal Local Alignments across Multiple Scoring Schemes” in Proc. of WABI 2004 LNBI, vol. 3240, (SPRINGER-VERLAG BERLIN), 99-110.
Michael, M., Dieterich, C., & Stoye, J., 2004. Suboptimal Local Alignments across Multiple Scoring Schemes. In Proc. of WABI 2004. LNBI. no.3240 SPRINGER-VERLAG BERLIN, pp. 99-110.
M. Michael, C. Dieterich, and J. Stoye, “Suboptimal Local Alignments across Multiple Scoring Schemes”, Proc. of WABI 2004, LNBI, vol. 3240, SPRINGER-VERLAG BERLIN, 2004, pp.99-110.
Michael, M., Dieterich, C., Stoye, J.: Suboptimal Local Alignments across Multiple Scoring Schemes. Proc. of WABI 2004. LNBI. 3240, p. 99-110. SPRINGER-VERLAG BERLIN (2004).
Michael, Morris, Dieterich, Christoph, and Stoye, Jens. “Suboptimal Local Alignments across Multiple Scoring Schemes”. Proc. of WABI 2004. SPRINGER-VERLAG BERLIN, 2004.Vol. 3240. LNBI. 99-110.