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IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers Pseudoknots, leading to the capability of modeling a wide class of pseudOKnots and running quite fast.
PBSIM: PacBio reads simulator - toward accurate genome assembly
A read simulator, PBSIM, is developed that captures characteristic features of PacBio reads using either a model-based or sampling-based method, suggesting that a continuous long reads coverage depth of at least 15 in combination with a circular consensus sequencing coveragedepth of at at least 30 achieved extensive assembly results.
Parameters for accurate genome alignment
It is shown that γ-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases and enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases.
CentroidFold: a web server for RNA secondary structure prediction
- Kengo Sato, Michiaki Hamada, K. Asai, Toutai Mituyama
- Computer Science, BiologyNucleic Acids Res.
- 12 May 2009
The CentroidFold web server is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine which scores the best accuracy in the authors' benchmark results.
Prediction of RNA secondary structure using generalized centroid estimators
Novel estimators are proposed which improve the accuracy of secondary structure prediction of RNAs and represent extensions of the centroid estimators proposed in Ding et al. and Carvalho and Lawrence, and are applicable to a wide variety of problems in bioinformatics.
Comprehensive prediction of lncRNA–RNA interactions in human transcriptome
An integrated pipeline for predicting RNA–RNA interactions on the K computer, which is one of the fastest super-computers in the world, is developed and a database is developed that catalogs the predicted lncRNA– RNA interactions to provide fundamental information about the targets of lncRNAs.
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
- Michiaki Hamada, Kengo Sato, H. Kiryu, Toutai Mituyama, K. Asai
- Computer ScienceBioinform.
- 15 December 2009
A novel estimator for multiple alignments of structured RNAs is designed, which maximizes the expected sum-of-pairs score of a predicted alignment under a probability distribution of alignments given by marginalizing the Sankoff model and integrates the probabilistic consistency transformation on alignments into the proposed estimator.
Predictions of RNA secondary structure by combining homologous sequence information
It is found that the common secondary predictions sometimes give worse predictions for the secondary structure of a target sequence than the predictions from the individual target sequence, while the proposed method always gives good predictions for of target sequences in all tested cases.
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores
A generative model for quality scores is introduced, in which a hidden Markov Model with a latest model selection method, called factorized information criteria, is utilized, and this simulator successfully simulates reads that are consistent with real reads.
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
A deep learning framework, named DeepM6ASeq, is implemented to predict m6A-containing sequences and characterize surrounding biological features based on miCLIP-Seq data, which detects m 6A sites at single-base resolution and shows better performance than other machine learning classifiers.