Publication Details

Category Text Publication
Reference Category Book chapters
DOI 10.1007/978-3-642-21458-5_12
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.
Source Titel Lecture Notes in Computer Science
Year 2011
Department PROTEOM
Volume 6661
Page From 118
Page To 131
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.

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