KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences

Abstract Background The volume of viral genomic sequence data continues to increase rapidly. This is especially true for the smaller RNA viruses, which are relatively easy to sequence in large numbers. The data volumes cause a number of significant problems for research applications that require large multiple alignments of essentially complete genomes, which are of the order of 10 kb. Findings We present a simple strategy to enable the creation of large quasi-multiple sequence alignments from pairwise alignment data. This process is suitable for large, closely related sequences such as the polyproteins of dengue viruses, which need the insertion of very few indels. Conclusion The quasi-multiple sequence alignments generated by KISSa are sufficiently accurate to support tree-based genome selection for interactive bioinformatics analysis tools. The speed of this process is critical to providing an interactive experience for the user.