Cargando…

Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform

Recently we presented a frequentist dynamic programming (DP) approach for multiple sequence alignment based on the explicit model of indel evolution Poisson Indel Process (PIP). This phylogeny-aware approach produces evolutionary meaningful gap patterns and is robust to the ‘over-alignment’ bias. De...

Descripción completa

Detalles Bibliográficos
Autores principales:	Maiolo, Massimo, Ulzega, Simone, Gil, Manuel, Anisimova, Maria
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2020
Materias:	Methods Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671320/ https://www.ncbi.nlm.nih.gov/pubmed/33575636 http://dx.doi.org/10.1093/nargab/lqaa092

Ejemplares similares

Progressive multiple sequence alignment with indel evolution
por: Maiolo, Massimo, et al.
Publicado: (2018)

ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process
por: Maiolo, Massimo, et al.
Publicado: (2021)

Ultra-large alignments using phylogeny-aware profiles
por: Nguyen, Nam-phuong D., et al.
Publicado: (2015)

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
por: Grytten, Ivar, et al.
Publicado: (2022)

ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process
por: Jowkar, Gholamhossein, et al.
Publicado: (2022)

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
por: Yang, Rendong, et al.
Publicado: (2015)

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions
por: Loewenthal, Gil, et al.
Publicado: (2021)

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
por: Kaufmann, Tom L., et al.
Publicado: (2022)

Log Transformation Improves Dating of Phylogenies
por: Mai, Uyen, et al.
Publicado: (2020)

Predicting the effects of frameshifting indels
por: Hu, Jing, et al.
Publicado: (2012)

PHACT: Phylogeny-Aware Computing of Tolerance for Missense Mutations
por: Kuru, Nurdan, et al.
Publicado: (2022)

Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences
por: Mirsky, Alexander, et al.
Publicado: (2015)

Accurate quantification of lipid species affected by isobaric overlap in Fourier-transform mass spectrometry
por: Höring, Marcus, et al.
Publicado: (2021)

NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks
por: Ahsan, Mian Umair, et al.
Publicado: (2021)

The multiple alignments of very short sequences
por: Takács, Kristóf, et al.
Publicado: (2021)

New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs
por: Barton, Henry J, et al.
Publicado: (2018)

Graph-based modeling of tandem repeats improves global multiple sequence alignment
por: Szalkowski, Adam M., et al.
Publicado: (2013)

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
por: Nadeau, Sarah, et al.
Publicado: (2022)

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels
por: Zhao, Huiying, et al.
Publicado: (2013)

SvABA: genome-wide detection of structural variants and indels by local assembly
por: Wala, Jeremiah A., et al.
Publicado: (2018)

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
por: Köster, Johannes, et al.
Publicado: (2020)

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
por: Yuan, Ke, et al.
Publicado: (2015)

Sampling Trajectories for the Short-Time Fourier Transform
por: Speckbacher, Michael
Publicado: (2022)

Fast and sensitive detection of indels induced by precise gene targeting
por: Yang, Zhang, et al.
Publicado: (2015)

MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning
por: Li, Chang, et al.
Publicado: (2022)

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
por: Löytynoja, Ari, et al.
Publicado: (2010)

Tables of Fourier transforms and Fourier transforms of distributions
por: Oberhettinger, Fritz
Publicado: (1990)

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
por: Redelings, Benjamin D, et al.
Publicado: (2007)

Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels
por: Pedersen, Brent S, et al.
Publicado: (2022)

The Fourier-transform infrared spectroscopy-based method as a new typing tool for Candida parapsilosis clinical isolates
por: De Carolis, Elena, et al.
Publicado: (2023)

NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods
por: Roddy, Aideen C, et al.
Publicado: (2019)

The Effect of Nonreversibility on Inferring Rooted Phylogenies
por: Cherlin, Svetlana, et al.
Publicado: (2018)

A population model for genotyping indels from next-generation sequence data
por: Shao, Haojing, et al.
Publicado: (2013)

Fast and robust multiple sequence alignment with phylogeny-aware gap placement
por: Szalkowski, Adam M
Publicado: (2012)

Fourier transforms
por: Sneddon, Ian Naismith
Publicado: (1995)

Fourier transforms
por: Sneddon, Ian Naismith
Publicado: (1951)

Placing Ancient DNA Sequences into Reference Phylogenies
por: Martiniano, Rui, et al.
Publicado: (2022)

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome
por: Krawitz, Peter M, et al.
Publicado: (2014)

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
por: Upham, Nathan S., et al.
Publicado: (2019)

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
por: Homer, Nils, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_fnd2d8lfbvqed04hlckkgnfn41