Abstract. This paper addresses the problem of aligning multiple sequences of non-coding RNA genes. We approach this problem with the biologically motivated paradigm that scoring of...
Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for ...
Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Ander...
Background: A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score ...
Andreas Bremges, Stefanie Schirmer, Robert Giegeri...
In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence ...
During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignmen...