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Efficient estimation of emission probabilities in profile hidden Markov models.

Ahola, Virpi ; Aittokallio, Tero ; Uusipaikka, Esa and Vihinen, Mauno LU (2003) In Bioinformatics 19(18). p.2359-2368
Abstract
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.
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Sequence Alignment: methods, Proteins: classification, Proteins: chemistry, Enzymes: classification, Enzymes: chemistry, Amino Acids: chemistry, Amino Acids: classification, Sequence Analysis, Protein: methods
in
Bioinformatics
volume
19
issue
18
pages
2359 - 2368
publisher
Oxford University Press
external identifiers
  • pmid:14668219
  • scopus:0347513228
ISSN
1367-4803
language
English
LU publication?
no
id
9244b092-8e2d-4ed5-9c55-c514aa8f75fd (old id 3635527)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/14668219?dopt=Abstract
date added to LUP
2016-04-04 07:54:29
date last changed
2020-04-15 02:32:05
@article{9244b092-8e2d-4ed5-9c55-c514aa8f75fd,
  abstract     = {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.},
  author       = {Ahola, Virpi and Aittokallio, Tero and Uusipaikka, Esa and Vihinen, Mauno},
  issn         = {1367-4803},
  language     = {eng},
  number       = {18},
  pages        = {2359--2368},
  publisher    = {Oxford University Press},
  series       = {Bioinformatics},
  title        = {Efficient estimation of emission probabilities in profile hidden Markov models.},
  url          = {http://www.ncbi.nlm.nih.gov/pubmed/14668219?dopt=Abstract},
  volume       = {19},
  year         = {2003},
}