Chaining sequence/structure seeds for computing RNA similarity

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Laetitia BourgeadeJulien Allali

Abstract

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; and then (iii) completing the alignment using an anchor-based exact alignment algorithm. We apply our method on the benchmark Bralibase2.1 and compare its accuracy and efficiency with the exact method LocARNA and its recent seeds-based speed-up ExpLoc-P. Our pipeline RNA-unchained greatly improves computation time of LocARNA and is comparable to the one of ExpLoc-P, while improving the overall accuracy of the final alignments.

References

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Sep 10, 2013·BMC Bioinformatics·Cuncong Zhong, Shaojie Zhang

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Citations

Mar 18, 2016·Briefings in Bioinformatics·Benedikt LöwesRobert Giegerich

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Software Mentioned

Gardenia
Exploc
DeclareMathSizes
RNAsubopt
Infernal
ExpLocP
RNAforester
RNA
RNAshapes
LocARNA

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