2008
DOI: 10.1093/bioinformatics/btn601
|View full text |Cite
|
Sign up to set email alerts
|

Prediction of RNA secondary structure using generalized centroid estimators

Abstract: Supporting information and the CentroidFold software are available online at: http://www.ncrna.org/software/centroidfold/.

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
4
1

Citation Types

1
280
0

Year Published

2012
2012
2023
2023

Publication Types

Select...
5
1

Relationship

1
5

Authors

Journals

citations
Cited by 208 publications
(281 citation statements)
references
References 23 publications
1
280
0
Order By: Relevance
“…For the updated base-pairing probability matrix, the c-centroid estimator (Hamada et al, 2009b) was employed to predict a secondary structure from the BPPM. More specifically, we maximize the sum of the (updated) base-pairing probabilities for base pairs in the predicted secondary structure, in which base pairs whose probability is larger than 1/(c + 1) are allowed to form a base pair (Hamada et al, 2009b). The c is a parameter used to adjust the balance between sensitivity and positive predictive value of predicted base-pairs (a smaller c produces fewer base pairs).…”
Section: Computational Experimentsmentioning
confidence: 99%
See 4 more Smart Citations
“…For the updated base-pairing probability matrix, the c-centroid estimator (Hamada et al, 2009b) was employed to predict a secondary structure from the BPPM. More specifically, we maximize the sum of the (updated) base-pairing probabilities for base pairs in the predicted secondary structure, in which base pairs whose probability is larger than 1/(c + 1) are allowed to form a base pair (Hamada et al, 2009b). The c is a parameter used to adjust the balance between sensitivity and positive predictive value of predicted base-pairs (a smaller c produces fewer base pairs).…”
Section: Computational Experimentsmentioning
confidence: 99%
“…This indicates that the performance for e = 0 was worse than that for e s 0 in a part of sensitivity-PPV curve, which indicates that a non-zero e value could have the potential to improve the prediction accuracy when constraints include noise. The c-centroid estimators (Hamada et al, 2009b) are used when estimating secondary structures from the updated basepairing probability matrix. We utilized the S151 Rfam dataset in this experiment, and constraints are given according to reference secondary structures.…”
Section: Computational Experimentsmentioning
confidence: 99%
See 3 more Smart Citations