Alignment of Sequences Allowing for Non-overlapping Unbalanced Translocations of Adjacent Factors

Unbalanced translocations take place when two unequal chromosome sub-sequences swap, resulting in an altered genetic sequence. Such large-scale gene modification are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity. However, despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of aligning sequences allowing for this kind of modification. In this paper we investigate the sequence alignment problem when the edit operations are non-overlapping unbalanced translocations of adjacent factors. Specifically, we present an alignment algorithm for the problem working in $$\mathcal {O}(m^3)$$ -time and $$\mathcal {O}(m^3)$$ -space, where m is the length of the involved sequences. To the best of our knowledge this is the first solution in literature for the alignment problem allowing for unbalanced translocations of factors.