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Phylogenetic footprinting and consistent sets of local aligments

 
: Otto, W.; Stadler, P.F.; Prohaska, S.J.

:

Giancarlo, R.:
Combinatorial pattern matching. Proceedings : 22nd annual symposium, CPM 2011, Palermo, Italy, June 27-29, 2011
Heidelberg: Springer, 2011 (Lecture Notes in Computer Science 6661)
ISBN: 3-642-21457-6
ISBN: 978-3-642-21457-8
ISBN: 978-3-642-21458-5
ISSN: 0302-9743
pp.118-131
Annual Symposium on Combinatorial Pattern Matching (CPM) <22, 2011, Palermo>
English
Conference Paper
Fraunhofer IZI ()

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.

: http://publica.fraunhofer.de/documents/N-189690.html