Cargando…

Software.ncrna.org: web servers for analyses of RNA sequences

We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individua...

Descripción completa

Detalles Bibliográficos
Autores principales:	Asai, Kiyoshi, Kiryu, Hisanori, Hamada, Michiaki, Tabei, Yasuo, Sato, Kengo, Matsui, Hiroshi, Sakakibara, Yasubumi, Terai, Goro, Mituyama, Toutai
Formato:	Texto
Lenguaje:	English
Publicado:	Oxford University Press 2008
Materias:	Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447773/ https://www.ncbi.nlm.nih.gov/pubmed/18440970 http://dx.doi.org/10.1093/nar/gkn222

Ejemplares similares

Predictions of RNA secondary structure by combining homologous sequence information
por: Hamada, Michiaki, et al.
Publicado: (2009)

CentroidFold: a web server for RNA secondary structure prediction
por: Sato, Kengo, et al.
Publicado: (2009)

Directed acyclic graph kernels for structural RNA analysis
por: Sato, Kengo, et al.
Publicado: (2008)

Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features
por: Terai, Goro, et al.
Publicado: (2012)

Discovery of short pseudogenes derived from messenger RNAs
por: Terai, Goro, et al.
Publicado: (2010)

Rtools: a web server for various secondary structural analyses on single RNA sequences
por: Hamada, Michiaki, et al.
Publicado: (2016)

A fast structural multiple alignment method for long RNA sequences
por: Tabei, Yasuo, et al.
Publicado: (2008)

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
por: Mituyama, Toutai, et al.
Publicado: (2009)

Generalized Centroid Estimators in Bioinformatics
por: Hamada, Michiaki, et al.
Publicado: (2011)

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data
por: Fukunaga, Tsukasa, et al.
Publicado: (2014)

Comprehensive prediction of lncRNA–RNA interactions in human transcriptome
por: Terai, Goro, et al.
Publicado: (2016)

Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions
por: Saito, Yutaka, et al.
Publicado: (2015)

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions
por: Saito, Yutaka, et al.
Publicado: (2014)

Improving the accuracy of predicting secondary structure for aligned RNA sequences
por: Hamada, Michiaki, et al.
Publicado: (2011)

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
por: Hamada, Michiaki, et al.
Publicado: (2010)

Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility
por: Terai, Goro, et al.
Publicado: (2020)

QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity
por: Terai, Goro, et al.
Publicado: (2022)

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome
por: Iwakiri, Junichi, et al.
Publicado: (2017)

Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells
por: Saito, Yutaka, et al.
Publicado: (2017)

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
por: Afiahayati,, et al.
Publicado: (2015)

An extended genovo metagenomic assembler by incorporating paired-end information
por: , Afiahayati, et al.
Publicado: (2013)

minepath.org: a free interactive pathway analysis web server
por: Koumakis, Lefteris, et al.
Publicado: (2017)

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
por: Sato, Kengo, et al.
Publicado: (2011)

Robust and accurate prediction of noncoding RNAs from aligned sequences
por: Saito, Yutaka, et al.
Publicado: (2010)

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
por: Saito, Yutaka, et al.
Publicado: (2011)

A Max-Margin Model for Predicting Residue—Base Contacts in Protein–RNA Interactions
por: Kashiwagi, Shunya, et al.
Publicado: (2021)

RNA secondary structure prediction using deep learning with thermodynamic integration
por: Sato, Kengo, et al.
Publicado: (2021)

Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots
por: Akiyama, Manato, et al.
Publicado: (2022)

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
por: Hamada, Michiaki, et al.
Publicado: (2011)

Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model
por: Takizawa, Hiroki, et al.
Publicado: (2020)

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
por: Kato, Yuki, et al.
Publicado: (2010)

Improved Measurements of RNA Structure Conservation with Generalized Centroid Estimators
por: Okada, Yohei, et al.
Publicado: (2011)

Adjacent Nucleotide Dependence in ncRNA and Order-1 SCFG for ncRNA Identification
por: Wong, Thomas K. F., et al.
Publicado: (2010)

A Keystone for ncRNA
por: Hacisuleyman, Ezgi, et al.
Publicado: (2012)

Shape-based alignment of genomic landscapes in multi-scale resolution
por: Ashida, Hiroki, et al.
Publicado: (2012)

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs
por: Yonemoto, Haruka, et al.
Publicado: (2013)

Efficient calculation of exact probability distributions of integer features on RNA secondary structures
por: Mori, Ryota, et al.
Publicado: (2014)

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores
por: Ono, Yukiteru, et al.
Publicado: (2020)

PBSIM3: a simulator for all types of PacBio and ONT long reads
por: Ono, Yukiteru, et al.
Publicado: (2022)

Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network
por: Wang, Y, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_j91q3nb0n1q6em82ot4c2i2824