Cargando…

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rangel-Pineros, Guillermo, Almeida, Alexandre, Beracochea, Martin, Sakharova, Ekaterina, Marz, Manja, Reyes Muñoz, Alejandro, Hölzer, Martin, Finn, Robert D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2023
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10491390/ https://www.ncbi.nlm.nih.gov/pubmed/37639475 http://dx.doi.org/10.1371/journal.pcbi.1011422

Ejemplares similares

Smart Annotation of Cyclic Data Using Hierarchical Hidden Markov Models
por: Martindale, Christine F., et al.
Publicado: (2017)

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
por: Hölzer, Martin, et al.
Publicado: (2019)

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”
por: Hölzer, Martin, et al.
Publicado: (2017)

Multi-scale chromatin state annotation using a hierarchical hidden Markov model
por: Marco, Eugenio, et al.
Publicado: (2017)

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi
por: Sperschneider, Jana, et al.
Publicado: (2013)

Specialized Hidden Markov Model Databases for Microbial Genomics
por: Gollery, Martin
Publicado: (2003)

Inference in Hidden Markov Models
por: Cappe, Olivier
Publicado: (2005)

Hidden Markov Modeling with HMMTeacher
por: Fuentes-Beals, Camilo, et al.
Publicado: (2022)

Hidden Markov Model-Based Smart Annotation for Benchmark Cyclic Activity Recognition Database Using Wearables †
por: Martindale, Christine F., et al.
Publicado: (2019)

Hidden Markov Model Variants and their Application
por: Winters-Hilt, Stephen
Publicado: (2006)

Hidden Markov models: estimation and control
por: Elliott, Robert J, et al.
Publicado: (1995)

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
por: Kumar, Surendra, et al.
Publicado: (2011)

MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences
por: Morais, Diego A. A., et al.
Publicado: (2022)

Scalable Bayesian Inference for Coupled Hidden Markov and Semi-Markov Models
por: Touloupou, Panayiota, et al.
Publicado: (2019)

Analysis of an optimal hidden Markov model for secondary structure prediction
por: Martin, Juliette, et al.
Publicado: (2006)

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle
por: Zacher, Benedikt, et al.
Publicado: (2014)

Error statistics of hidden Markov model and hidden Boltzmann model results
por: Newberg, Lee A
Publicado: (2009)

Predicting enhancers in mammalian genomes using supervised hidden Markov models
por: Zehnder, Tobias, et al.
Publicado: (2019)

Approximating Hidden Gaussian Markov Random Fields
por: Rue, H, et al.
Publicado: (2003)

Epitope Discovery with Phylogenetic Hidden Markov Models
por: Lacerda, Miguel, et al.
Publicado: (2010)

Hidden Markov processes: theory and applications to biology
por: Vidyasagar, M
Publicado: (2014)

Estimating Empirical Codon Hidden Markov Models
por: De Maio, Nicola, et al.
Publicado: (2013)

Scanpath modeling and classification with hidden Markov models
por: Coutrot, Antoine, et al.
Publicado: (2017)

Modelling reassurances of clinicians with hidden Markov models
por: Popov, Valentin, et al.
Publicado: (2019)

SilentMutations (SIM): A tool for analyzing long-range RNA–RNA interactions in viral genomes and structured RNAs
por: Desirò, Daniel, et al.
Publicado: (2019)

Profile Comparer: a program for scoring and aligning profile hidden Markov models
por: Madera, Martin
Publicado: (2008)

Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks
por: Mock, Florian, et al.
Publicado: (2022)

Coupling spectral analysis and hidden Markov models for the segmentation of behavioural patterns
por: Heerah, Karine, et al.
Publicado: (2017)

Dfam: a database of repetitive DNA based on profile hidden Markov models
por: Wheeler, Travis J., et al.
Publicado: (2013)

A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
por: Mostajo, Nelly F, et al.
Publicado: (2019)

Hidden semi-Markov models: theory, algorithms and applications
por: Yu, Shun-Zheng
Publicado: (2016)

Constrained hidden Markov models for population-based haplotyping
por: Landwehr, Niels, et al.
Publicado: (2007)

Riboswitch Detection Using Profile Hidden Markov Models
por: Singh, Payal, et al.
Publicado: (2009)

Disease surveillance using a hidden Markov model
por: Watkins, Rochelle E, et al.
Publicado: (2009)

Hidden Markov Models and their Applications in Biological Sequence Analysis
por: Yoon, Byung-Jun
Publicado: (2009)

Hidden Markov Models for Evolution and Comparative Genomics Analysis
por: Bykova, Nadezda A., et al.
Publicado: (2013)

Hidden Markov Models: The Best Models for Forager Movements?
por: Joo, Rocio, et al.
Publicado: (2013)

A coupled hidden Markov model for disease interactions
por: Sherlock, Chris, et al.
Publicado: (2013)

Tuberculosis Surveillance Using a Hidden Markov Model
por: Rafei, A, et al.
Publicado: (2012)

Recent Applications of Hidden Markov Models in Computational Biology
por: Choo, Khar Heng, et al.
Publicado: (2004)

Cannot write session to /tmp/vufind_sessions/sess_slaa1s5p87qbt65b3bgh5muo70