Tracker2 - Alignment Concictency and Footprint Detection: Phylogenetic footprinting and consistent sets of local aligments. 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.
References in zbMATH (referenced in 1 article )
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- Otto, Wolfgang; Stadler, Peter F.; Prohaska, Sonja J.: Phylogenetic footprinting and consistent sets of local aligments (2011)