Name
Title | ||
|---|---|---|
Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. |
Abstract | ||
|---|---|---|
The analysis of the sequence-structure relationship in RNA molecules is not only essential for evolutionary studies but also for concrete applications such as error-correction in next generation sequencing (NGS) technologies. The prohibitive sizes of the mutational and conformational landscapes, combined with the volume of data to process, require efficient algorithms to compute sequence-structure properties. In this article, we address the correction of NGS errors by calculating which mutations most increase the likelihood of a sequence to a given structure and RNA family. We introduce RNApyro, an efficient, linear time and space inside-outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given as a multiple sequence alignment with a consensus structure. We develop a scoring scheme combining classical stacking base-pair energies to novel isostericity scores and apply our techniques to correct pointwise errors in 5s and 16s rRNA sequences. Our results suggest that RNApyro is a promising algorithm to complement existing tools in the NGS error-correction pipeline. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1089/cmb.2013.0085 | JOURNAL OF COMPUTATIONAL BIOLOGY |
Keywords | Field | DocType |
mutations,RNA,secondary structure | RNA,DNA sequencing,Pyrosequencing,Bioinformatics,Time complexity,Multiple sequence alignment,Protein secondary structure,Mathematics,Evolutionary information,Pointwise | Journal |
Volume | Issue | ISSN |
20.0 | 11 | 1066-5277 |
Citations | PageRank | References |
0 | 0.34 | 8 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Vladimir Reinharz | 1 | 22 | 3.39 |
| Yann Ponty | 2 | 249 | 25.67 |
| Jérôme Waldispühl | 3 | 111 | 16.24 |