title: NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.
abstract: CONCLUSIONS
  Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings.
  
  
  BACKGROUND
  Downloable and web-based versions of NASP are freely available at http://web.cbio.uct.ac.za/~yves/nasp_portal.php
  
  
  BACKGROUND
  yves@cbio.uct.ac.za
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Biology Group, Department of Clinical Laboratory Sciences, IIDMM, University of Cape Town, Observatory, Cape Town, South Africa. yves@cbio.uct.ac.za
authors.forename: J Y
authors.initials: JY
authors.lastname: Semegni
authors.forename: M
authors.initials: M
authors.lastname: Wamalwa
authors.forename: R
authors.initials: R
authors.lastname: Gaujoux
authors.forename: G W
authors.initials: GW
authors.lastname: Harkins
authors.forename: A
authors.initials: A
authors.lastname: Gray
authors.forename: D P
authors.initials: DP
authors.lastname: Martin
mesh_terms: D004247:DNA / Q000737:chemistry*; D019143:Evolution, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D009711:Nucleotides; D012313:RNA; D004247:DNA