Results: We describe a new method to compare a query RNA with a static set of target RNAs. Our method is based on (i) a static indexing of the sequence/structure seeds of the target RNAs, (ii) searching the target RNAs by detecting seeds of the query present in the target, chaining these seeds in promising candidate homologs, then (iii) completing the alignment using an anchor-based exact alignment algorithm. We apply our method on the benchmark Bralibase 2.1 and compare its accuracy and efficiency with the exact method LocaRNA and its recent seeds-based speed-up ExpLoc-P. Our pipeline RNA-unchained computes constraints that greatly improve computation time of LocaRNA and is comparable to the one of ExpLoc-P, while improving the overall accuracy of the final alignments.
Availability: RNA-unchained is available at http://bioinfo.labri.fr/tools/RNA-unchained
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