title: Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
abstract: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing.
  
  
  
  To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000-6000 nucleotides improve execution up to a factor of five.
  
  
  
  The Foldalign software and the web server are available at http://rth.dk/resources/foldalign
  
  
  
  gorodkin@rth.dk
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and Department of Computer Science, University of Brasilia, Brasília, DF, Brazil.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sundfeld
authors.affiliation: Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and.
authors.forename: Jakob H
authors.initials: JH
authors.lastname: Havgaard
authors.affiliation: Department of Computer Science, University of Brasilia, Brasília, DF, Brazil.
authors.forename: Alba C M A
authors.initials: AC
authors.lastname: de Melo
authors.affiliation: Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and.
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
mesh_terms: D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D012313:RNA