Efficient estimation of emission probabilities in profile hidden Markov models.

Research output: Contribution to journalArticle


Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that the conserved amino acids are not emphasized, but signal and noise are treated equally. For this reason, the number of estimated emission parameters is often enormous. Focusing the analysis on conserved residues only should increase the accuracy of sequence database search.


External organisations
  • External Organization - Unknown
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Bioinformatics and Systems Biology


  • Sequence Alignment: methods, Proteins: classification, Proteins: chemistry, Enzymes: classification, Enzymes: chemistry, Amino Acids: chemistry, Amino Acids: classification, Sequence Analysis, Protein: methods
Original languageEnglish
Pages (from-to)2359-2368
Issue number18
Publication statusPublished - 2003
Publication categoryResearch
Externally publishedYes