TY - JOUR
T1 - Direct updating of an RNA base-pairing probability matrix with marginal probability constraints
AU - Hamada, Michiaki
PY - 2012/12/1
Y1 - 2012/12/1
N2 - A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning-based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented.
AB - A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning-based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented.
KW - RNA
KW - algorithms
KW - alignment
KW - secondary structure
KW - sequence analysis
UR - http://www.scopus.com/inward/record.url?scp=84870686237&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84870686237&partnerID=8YFLogxK
U2 - 10.1089/cmb.2012.0215
DO - 10.1089/cmb.2012.0215
M3 - Article
C2 - 23210474
AN - SCOPUS:84870686237
VL - 19
SP - 1265
EP - 1276
JO - Journal of Computational Biology
JF - Journal of Computational Biology
SN - 1066-5277
IS - 12
ER -