Cargando…

Human contamination in bacterial genomes has created thousands of spurious proteins

Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes...

Descripción completa

Detalles Bibliográficos
Autores principales:	Breitwieser, Florian P., Pertea, Mihaela, Zimin, Aleksey V., Salzberg, Steven L.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2019
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581058/ https://www.ncbi.nlm.nih.gov/pubmed/31064768 http://dx.doi.org/10.1101/gr.245373.118

Ejemplares similares

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
por: Pertea, Mihaela, et al.
Publicado: (2018)

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
por: Chao, Kuan-Hao, et al.
Publicado: (2023)

Transcriptome assembly from long-read RNA-seq alignments with StringTie2
por: Kovaka, Sam, et al.
Publicado: (2019)

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
por: Wood, Derrick E, et al.
Publicado: (2012)

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
por: Zimin, Aleksey V., et al.
Publicado: (2020)

The SAMBA tool uses long reads to improve the contiguity of genome assemblies
por: Zimin, Aleksey V., et al.
Publicado: (2022)

Assembly and annotation of an Ashkenazi human reference genome
por: Shumate, Alaina, et al.
Publicado: (2020)

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
por: Guo, Alina, et al.
Publicado: (2023)

Detection of lineage-specific evolutionary changes among primate species
por: Pertea, Mihaela, et al.
Publicado: (2011)

Between a chicken and a grape: estimating the number of human genes
por: Pertea, Mihaela, et al.
Publicado: (2010)

Do-it-yourself genetic testing
por: Salzberg, Steven L, et al.
Publicado: (2010)

Between a chicken and a grape: estimating the number of human genes
por: Pertea, Mihaela, et al.
Publicado: (2010)

OperonDB: a comprehensive database of predicted operons in microbial genomes
por: Pertea, Mihaela, et al.
Publicado: (2009)

DIAMUND: Direct Comparison of Genomes to Detect Mutations
por: Salzberg, Steven L, et al.
Publicado: (2014)

Gene-Environment Dependence Creates Spurious Gene-Environment Interaction
por: Dudbridge, Frank, et al.
Publicado: (2014)

Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
por: Trapnell, Cole, et al.
Publicado: (2010)

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments
por: Varabyou, Ales, et al.
Publicado: (2021)

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
por: Chang, Tsung-Cheng, et al.
Publicado: (2015)

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
por: Pertea, Mihaela, et al.
Publicado: (2007)

Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content
por: Kostadinov, Rumen, et al.
Publicado: (2016)

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
por: Varabyou, Ales, et al.
Publicado: (2020)

Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage
por: Varabyou, Ales, et al.
Publicado: (2023)

Metagenomic classification with KrakenUniq on low-memory computers
por: Pockrandt, Christopher, et al.
Publicado: (2022)

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
por: Florea, Liliana, et al.
Publicado: (2013)

Removing contaminants from databases of draft genomes
por: Lu, Jennifer, et al.
Publicado: (2018)

Splam: a deep-learning-based splice site predictor that improves spliced alignments
por: Chao, Kuan-Hao, et al.
Publicado: (2023)

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
por: Read, Andrew C., et al.
Publicado: (2020)

Spurious Generalization
Publicado: (1872)

On Spurious Consumption
Publicado: (1872)

Spurious Wines
Publicado: (1887)

Spurious Pregnancy
por: McVey, Bruce P.
Publicado: (1893)

Spurious History
Publicado: (1895)

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)
por: Luo, Ruibang, et al.
Publicado: (2017)

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
por: Allen, Jonathan E, et al.
Publicado: (2006)

Efficient decoding algorithms for generalized hidden Markov model gene finders
por: Majoros, William H, et al.
Publicado: (2005)

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum
por: Zimin, Aleksey V, et al.
Publicado: (2017)

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
por: Rubio, Alejandro, et al.
Publicado: (2020)

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection
por: Breitwieser, Florian P., et al.
Publicado: (2015)

The genome of the American groundhog, Marmota monax
por: Puiu, Daniela, et al.
Publicado: (2020)

Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome
por: Zimin, Aleksey V., et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_qu00rru72951m99pn83b23aoik