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:
https://lup.lub.lu.se/record/3635527
- author
- Ahola, Virpi
; Aittokallio, Tero
; Uusipaikka, Esa
and Vihinen, Mauno
LU
- publishing date
- 2003
- 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
- 2022-01-29 02:48:59
@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}},
keywords = {{Sequence Alignment: methods; Proteins: classification; Proteins: chemistry; Enzymes: classification; Enzymes: chemistry; Amino Acids: chemistry; Amino Acids: classification; Sequence Analysis; Protein: methods}},
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}},
}