This review provides an overview on the development of Multiple sequence alignment
(MSA) methods and their main applications. It is focused on progress made over the past …

This review focuses on recent trends in multiple sequence alignment tools. It describes the
latest algorithmic improvements including the extension of consistency-based methods to …

Constraint programming is a powerful paradigm for solving combinatorial search problems
that draws on a wide range of techniques from artificial intelligence, computer science …

Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic
regions containing potential structural ncRNAs. The analysis of these data requires highly …

Background The prediction of a consensus structure for a set of related RNAs is an important
first step for subsequent analyses. RNAalifold, which computes the minimum energy …

The RFAM database defines families of ncRNAs by means of sequence similarities that are
sufficient to establish homology. In some cases, such as microRNAs and box H/ACA …

Background In sequence analysis the multiple alignment builds the fundament of all
proceeding analyses. Errors in an alignment could strongly influence all succeeding …

For evolutionary comparisons, phylogenetics and evaluation of potential interbreeding taxa
of a species, various loci have served for animals and plants and protistans. One [second …

Background The function of a noncoding RNA sequence is mainly determined by its
secondary structure and therefore a family of noncoding RNA sequences is much more …

Integrative taxonomy is an approach for defining species and genera by taking phylogenetic,
morphological, physiological, and ecological data into account. This approach is appropriate …