title: Reconstruction of ancestral RNA sequences under multiple structural constraints.
abstract: Secondary 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.
  
  
  
  In 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.
  
  
  
  We 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.
  
  
  
  Our 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 .
authors.affiliation: School of Computer Science, McGill University, Montreal, H3A 0E9, Canada.|Department of Computer Science, University of Manitoba, Winnipeg, R3T 2N2, Canada.
authors.forename: Olivier
authors.initials: O
authors.lastname: Tremblay-Savard
authors.affiliation: School of Computer Science, McGill University, Montreal, H3A 0E9, Canada.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Reinharz
authors.affiliation: School of Computer Science, McGill University, Montreal, H3A 0E9, Canada. jeromew@cs.mcgill.ca.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Waldispühl
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D030541:Databases, Genetic; D020407:Internet; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D022661:RNA, Untranslated / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D014584:User-Computer Interface
chemical_list: D022661:RNA, Untranslated
keywords: Algorithm; Ancestor reconstruction; Evolution; Phylogeny; RNA; Secondary structure