Publication Details

Reference Category Book chapters
DOI / URL link
Title (Primary) Phylogenetic footprinting and consistent sets of local aligments
Title (Secondary) Combinatorial Pattern Matching : 22nd Annual Symposium, CPM 2011, Palermo, Italy, June 27-29, 2011. Proceedings
Author Otto, W.; Stadler, P.F.; Prohaska, S.J.;
Publisher Giancarlo, R.; Manzini, G.;
Journal Lecture Notes in Computer Science
Year 2011
Department PROTEOM;
Volume 6661
Language englisch;
Keywords alignment consistency; phylogenetic footprinting; combinatorial optimization; tracker2
Abstract

The problem of constructing alternative local multiple sequence alignments from a collection of local pairwise alignments arises naturally in phylogenetic footprinting, a technique used to identify regulatory elements by comparative sequence analysis. Based on a theoretical discussion of the problem we devise an efficient heuristic and introduce the software tool tracker2 for this task. Tests on both biological and random data demonstrated the heuristic yields excellent results at very short runtimes.

ID 12072
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=12072
Otto, W., Stadler, P.F., Prohaska, S.J. (2011):
Phylogenetic footprinting and consistent sets of local aligments
In: Giancarlo, R., Manzini, G. (eds.)
Combinatorial Pattern Matching : 22nd Annual Symposium, CPM 2011, Palermo, Italy, June 27-29, 2011. Proceedings
Lect. Notes Comput. Sci. 6661
Springer, Berlin, Heidelberg, New York, p. 118 - 131