title: A simple and fast secondary structure prediction method using hidden neural networks.
abstract: BACKGROUND
  In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural network for predicting the secondary structure elements in a 7-state local structure scheme and then optimizes the output using a hidden Markov model, which results in providing more information for the prediction.
  
  
  RESULTS
  YASPIN was compared with the current top-performing secondary structure prediction methods, such as PHDpsi, PROFsec, SSPro2, JNET and PSIPRED. The overall prediction accuracy on the independent EVA5 sequence set is comparable with that of the top performers, according to the Q3, SOV and Matthew's correlations accuracy measures. YASPIN shows the highest accuracy in terms of Q3 and SOV scores for strand prediction.
  
  
  BACKGROUND
  YASPIN is available on-line at the Centre for Integrative Bioinformatics website (http://ibivu.cs.vu.nl/programs/yaspinwww/) at the Vrije University in Amsterdam and will soon be mirrored on the Mathematical Biology website (http://www.mathbio.nimr.mrc.ac.uk) at the NIMR in London.
  
  
  BACKGROUND
  kxlin@nimr.mrc.ac.uk
authors.affiliation: Division of Mathematical Biology, The National Institute for Medical Research The Ridgeway, Mill Hill, London NW7 1AA, UK. kxlin@nimr.mrc.ac.uk
authors.forename: Kuang
authors.initials: K
authors.lastname: Lin
authors.forename: Victor A
authors.initials: VA
authors.lastname: Simossis
authors.forename: Willam R
authors.initials: WR
authors.lastname: Taylor
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D008390:Markov Chains; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins