GESTALT: Genomic Steiner Alignments

We describe GESTALT (GEnomic sequences STeiner ALignmenT), a public-domain suite of programs for generating multiple alignments of a set of biosequences.We allow the use of either of the two popular objectives, Tree Alignment or Sum-of-Pairs. The main distinguishing feature of our method is that the alignment is obtained via a tree in which the internal nodes (ancestors) are labeled by Steiner sequences for triples of the input sequences. Given lists of candidate labels for the ancestral sequences, we use dynamic programming to choose an optimal labeling under either objective function. Finally, the fully labeled tree of sequences is turned into into a multiple alignment. Enhancements in our implementation include the traditional space-saving ideas of Hirschberg as well as new data-packing techniques. The running-time bottleneck of computing exact Steiner sequences is handled by a highly effective but much faster heuristic alternative. Finally, other modules in the suite allow automatic generation of linear-program input files that can be used to compute new lower bounds on the optimal values. We also report on some preliminary computational experiments with GESTALT.