Reconstruction of ancestral RNA sequences under multiple structural constraints

BMC Genomics

Research

Vladimir Reinharz¹  Jérôme Waldispühl¹  Olivier Tremblay-Savard² 

[1] School of Computer Science, McGill University, H3A 0E9, Montreal, Canada;School of Computer Science, McGill University, H3A 0E9, Montreal, Canada;Department of Computer Science, University of Manitoba, R3T 2N2, Winnipeg, Canada;

关键词: RNA;    Secondary structure;    Ancestor reconstruction;    Evolution;    Phylogeny;    Algorithm;   

DOI  :  10.1186/s12864-016-3105-4

来源: Springer

【 摘 要 】

BackgroundSecondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors.MethodsIn this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families.ResultsWe test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database.ConclusionsOur results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement.

【 授权许可】

CC BY   
© The Author(s) 2016

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