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.

Conference Paper | Published | English

No fulltext has been uploaded

Author
; ;
Abstract
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.
Publishing Year
Conference
WABI 2004
Location
Bergen, Norway
ISSN
PUB-ID

Cite this

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, 3240, 99-110.
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.
This data publication is cited in the following publications:
This publication cites the following data publications:

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Search this title in

Google Scholar