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IGAUNA (Improved Global Sequence Alignment Using Non-exact Anchors)

With the sequencing of the entire genome for many species, bioinformaticians are increasingly relying on efficient whole genome alignment tools exhibiting both high sensitivity and specificity. We introduce and analyze IGAUNA (Improved Global Alignment Using Non-exact Anchors), a new global alignment algorithm based on GAUNA, which in comparison with the other state-of-the-art algorithms, almost always produces as good or better alignments with high sensitivity and specificity using less time and space. While those tools either find exact or close-to-exact matches as anchors, IGAUNA makes use of suffix trees to find both types of anchors depending on the instance: Exact anchors for very similar sequences and otherwise non-exact anchors that are obtained from a complicated set of techniques. In particular, IGAUNA can rapidly align sequences containing millions of bases on a standard PC where other similar programs are currently incapable of accomplishing such a task.