Abstract
Gene structure prediction is one of the most important problems in computational molecular biology. A combinatorial approach to the problem, denoted Gene Prediction via Spliced Alignment, was introduced by Gelfand, Mironov and Pevzner [5]. The method works by finding a set of blocks in a source genomic sequence S whose concatenation (splicing) fits a target gene T belonging to a homologous species. Let S,T and the candidate exons be sequences of size O(n). The innovative algorithm described in [5] yields an O(n 3) result for spliced alignment, regardless of filtration mode.
In this paper we suggest a new algorithm which targets the case where filtering has been applied to the data, resulting in a set of O(n) candidate exon blocks. Our algorithm yields an \(O(n^2 \sqrt{n})\) solution for this case.
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Kent, C., Landau, G.M., Ziv-Ukelson, M. (2005). On the Complexity of Sparse Exon Assembly. In: Apostolico, A., Crochemore, M., Park, K. (eds) Combinatorial Pattern Matching. CPM 2005. Lecture Notes in Computer Science, vol 3537. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11496656_18
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DOI: https://doi.org/10.1007/11496656_18
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