Cargando…

d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes

BACKGROUND: Structural annotation of genetic variants in the context of intermolecular interactions and protein stability can shed light onto mechanisms of disease-related phenotypes. Three-dimensional structures of related proteins in complexes with other proteins, nucleic acids, or ligands enrich...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gress, Alexander, Srikakulam, Sanjay K, Keller, Sebastian, Ramensky, Vasily, Kalinina, Olga V
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2022
Materias:	Technical Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9487898/ https://www.ncbi.nlm.nih.gov/pubmed/36130085 http://dx.doi.org/10.1093/gigascience/giac086

Ejemplares similares

StructMAn: annotation of single-nucleotide polymorphisms in the structural context
por: Gress, Alexander, et al.
Publicado: (2016)

YAMP: a containerized workflow enabling reproducibility in metagenomics research
por: Visconti, Alessia, et al.
Publicado: (2018)

ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
por: Piccolo, Stephen R, et al.
Publicado: (2020)

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake
por: Thompson, Luke R, et al.
Publicado: (2022)

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software
por: Mittal, Varun, et al.
Publicado: (2017)

NDER: A novel web application using annotated whole slide images for rapid improvements in human pattern recognition
por: Reder, Nicholas P., et al.
Publicado: (2016)

struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
por: Lloyd, Gavin Rhys, et al.
Publicado: (2020)

MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants
por: Srikakulam, Sanjay K, et al.
Publicado: (2023)

Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes
por: Gress, A, et al.
Publicado: (2017)

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission
por: Geib, Scott M, et al.
Publicado: (2018)

Container Profiler: Profiling resource utilization of containerized big data pipelines
por: Hoang, Varik, et al.
Publicado: (2023)

CABRA: Cluster and Annotate Blast Results Algorithm
por: Mier, Pablo, et al.
Publicado: (2016)

Bias-invariant RNA-sequencing metadata annotation
por: Wartmann, Hannes, et al.
Publicado: (2021)

Mantis: flexible and consensus-driven genome annotation
por: Queirós, Pedro, et al.
Publicado: (2021)

BioStructMap: a Python tool for integration of protein structure and sequence-based features
por: Guy, Andrew J, et al.
Publicado: (2018)

Salvaging Affymetrix probes after probe-level re-annotation
por: de Leeuw, Wim C, et al.
Publicado: (2008)

A collection of bioconductor methods to visualize gene-list annotations
por: Feng, Gang, et al.
Publicado: (2010)

VariantClassifier: A hierarchical variant classifier for annotated genomes
por: Li, Kelvin, et al.
Publicado: (2010)

AGOUTI: improving genome assembly and annotation using transcriptome data
por: Zhang, Simo V., et al.
Publicado: (2016)

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets
por: Hosseini, Parsa, et al.
Publicado: (2010)

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra()
por: Hulstaert, Niels, et al.
Publicado: (2013)

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
por: Hiltemann, Saskia, et al.
Publicado: (2014)

Leveraging multiple transcriptome assembly methods for improved gene structure annotation
por: Venturini, Luca, et al.
Publicado: (2018)

SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
por: Angelova, Nelina, et al.
Publicado: (2022)

CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis
por: Qiu, Xintao, et al.
Publicado: (2021)

Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls
por: Pedersen, Brent S, et al.
Publicado: (2019)

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
por: Brown, Stuart M, et al.
Publicado: (2019)

hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution
por: Jackson, Chris, et al.
Publicado: (2023)

Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics
por: Govender, Ireshyn Selvan, et al.
Publicado: (2023)

m6ASNP: a tool for annotating genetic variants by m(6)A function
por: Jiang, Shuai, et al.
Publicado: (2018)

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
por: Yu, Sung-Huan, et al.
Publicado: (2018)

A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study
por: Dudgeon, Sarah N., et al.
Publicado: (2021)

Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays
por: Mengual, Lourdes, et al.
Publicado: (2008)

Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data
por: Cullen, Jonah N, et al.
Publicado: (2023)

GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci
por: Fonseca, Pablo A S, et al.
Publicado: (2020)

Struct-f4: a Rcpp package for ancestry profile and population structure inference from f(4)-statistics
por: Librado, Pablo, et al.
Publicado: (2022)

Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences
por: Jaschob, Daniel, et al.
Publicado: (2015)

RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements
por: Osipova, Ekaterina, et al.
Publicado: (2019)

Whole Glenoid Reconstruction for Multidirectional Instability of the Shoulder
por: Zhao, Jinzhong
Publicado: (2021)

Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms
por: Reuveni, Eli, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_15qbnrqngferpk8got6j1tugk4