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Bioinformatics Advance Access originally published online on September 17, 2004
Bioinformatics 2005 21(2):152-159; doi:10.1093/bioinformatics/bth487
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.

A simple and fast secondary structure prediction method using hidden neural networks

Kuang Lin 1,*,{dagger}, Victor A. Simossis 2,{dagger}, Willam R. Taylor 1 and Jaap Heringa 2,3

1 Division of Mathematical Biology, The National Institute for Medical Research The Ridgeway, Mill Hill, London NW7 1AA, UK
2 Bioinformatics Section, Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands
3 Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands

*To whom correspondence should be addressed.

Motivation: 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.

Availability: 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.

Contact: kxlin{at}nimr.mrc.ac.uk


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