Abstract
We explore the problem of designing oligonucleotides that help locate organisms along a known phylogenetic tree. We develop a suffix-tree based algorithm to find such short sequences efficiently. Our algorithm requires O(Nm) time and O(N) space in the worst case where m is the number of the genomes classified by the phylogeny and N is their total length. We implemented our algorithm and used it to find these discriminating sequences in both small and large phylogenies. We believe our algorithm will have wide applications including: high-throughput classification and identification, oligo array design optimally differentiating genes in gene families, and markers for closely related strains and populations. It will also have scientific significance as a new way to assess the confidence in a given classification.
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Angelov, S., Harb, B., Kannan, S., Khanna, S., Kim, J., Wang, LS. (2004). Genome Identification and Classification by Short Oligo Arrays. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_34
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DOI: https://doi.org/10.1007/978-3-540-30219-3_34
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