ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores (Q31160615)

20 October 2017

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores (English)

1 reference

20 October 2017

1 reference

Luis Miguel Rodríguez-R

series ordinal

1 reference

Konstantinos T. Konstantinidis

20 October 2017

object named as

Konstantinos T Konstantinidis

0 references

Luis H Orellana

1 reference

20 October 2017

language of work or name

English

0 references

publication date

1 February 2017

1 reference

20 October 2017

Nucleic Acids Research

1 reference

20 October 2017

1 reference

20 October 2017

1 reference

20 October 2017

e14

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

20 October 2017

start time

9 February 2017

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

UProC: tools for ultra-fast protein domain classification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

GRASP: guided reference-based assembly of short peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Fast and sensitive protein alignment using DIAMOND

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

FunGene: the functional gene pipeline and repository

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Analysis Tool Web Services from the EMBL-EBI.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Structure, function and diversity of the healthy human microbiome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Grinder: a versatile amplicon and shotgun sequence simulator

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

A format for phylogenetic placements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Accelerated Profile HMM Searches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Taxonomic classification of metagenomic shotgun sequences with CARMA3.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

pROC: an open-source package for R and S+ to analyze and compare ROC curves

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

FragGeneScan: predicting genes in short and error-prone reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Insights into the effect of soil pH on N(2)O and N(2) emissions and denitrifier community size and activity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

BLAST+: architecture and applications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

A bioinformatician's guide to metagenomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Type-2 copper-containing enzymes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

MEGAN analysis of metagenomic data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Archaea predominate among ammonia-oxidizing prokaryotes in soils

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Isolation of an autotrophic ammonia-oxidizing marine archaeon

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Enzymology of the oxidation of ammonia to nitrite by bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5388429

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW900

21 January 2018

Identifiers

DOI

10.1093/NAR/GKW900

1 reference

20 October 2017

1 reference

20 October 2017

PubMed publication ID

28180325

1 reference