6. Prediction methods

Database search and prediction methods for protein sequences

  • Mitrophanov AY, Borodovsky M. Statistical significance in biological sequence analysis.Brief Bioinform. 2006 Mar;7(1):2-24.[PDF]
  • Altschul SF, Bundschuh R, Olsen R, Hwa T. The estimation of statistical parameters for local alignment score distributions.Nucleic Acids Res. 2001 Jan 15;29(2):351-61.[PDF]
  • Spang R, Vingron M. Statistics of large-scale sequence searching. Bioinformatics (Oxford, England). 1998;14(3):279-84. [PDF]
  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology. 2001;305(3):567-80. [PDF]
  • Tusnády GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics (Oxford, England). 2001;17(9):849-50. [PDF]
  • Olof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Locating proteins in the cell using TargetP, SignalP, and related tools. Nature Protocols 2, 953-971 (2007). [PDF]
  • Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. A Hidden Markov Model capable of predicting and discriminating β-barrel outer membrane proteins. BMC Bioinformatics, 2004, 5:29 [PDF]
  • Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. Journal of molecular biology. 2004;340(4):783-95. [PDF]
  • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. Journal of molecular biology. 1999;292(2):195-202. [PDF]
  • S. R. Eddy. Profile Hidden Markov Models. Bioinformatics, 14:755-763, 1998.[PDF]