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Published in:
2013 | OriginalPaper | Chapter
Using Carrillo-Lipman Approach to Speed up Simultaneous Alignment and Folding of RNA Sequences
Author : Mária Šimaľová
Published in: Adaptive and Natural Computing Algorithms
Publisher: Springer Berlin Heidelberg
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Multiple sequence alignment and RNA folding are two important tasks in the field of bioinformatics. Solving those problems simultaneously leads to biologically more significant results. The only one currently known precise algorithm (Sankoff) is too much computationaly expensive for such long sequences. In this work we introduce a new algorithm, that is a combination of well known Nussinov folding algorithm and Sankoff quadratic alignment algorithm and a speed-up for this algorithm that is inspired by the Carrillo-Lipman algorithm for the multiple sequence alignment problem. This approach may allow us to simultaneously align and fold more than two sequences in a better time than we can do it using the Sankoff algorithm.