(Q34394295)

1 August 2017

title

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides (English)

1 reference

1 August 2017

1 reference

Joel Berendzen

1

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1 August 2017

William J Bruno

2

1 reference

1 August 2017

Judith D Cohn

3

1 reference

1 August 2017

Nicolas W Hengartner

4

1 reference

1 August 2017

Cheryl R Kuske

5

1 reference

1 August 2017

Benjamin H McMahon

6

1 reference

1 August 2017

Murray A Wolinsky

7

1 reference

1 August 2017

Gary Xie

8

1 reference

1 August 2017

publication date

28 August 2012

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1 August 2017

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1 August 2017

volume

5

1 reference

1 August 2017

page(s)

460

1 reference

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

1 August 2017

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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Drivers of bacterial beta-diversity depend on spatial scale

6 July 2018

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6 July 2018

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6 July 2018

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SPHINX—an algorithm for taxonomic binning of metagenomic sequences

6 July 2018

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High Frequency of Horizontal Gene Transfer in the Oceans

6 July 2018

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Search and clustering orders of magnitude faster than BLAST

6 July 2018

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6 July 2018

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Deriving enzymatic and taxonomic signatures of metagenomes from short read data

6 July 2018

1 reference

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Predicting conserved protein motifs with Sub-HMMs.

6 July 2018

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Metagenomic sequencing of an in vitro-simulated microbial community

6 July 2018

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Artificial and natural duplicates in pyrosequencing reads of metagenomic data

6 July 2018

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Harnessing the power of the human microbiome

6 July 2018

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Environmental distribution of prokaryotic taxa

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Metagenome fragment classification using N-mer frequency profiles

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

FIGfams: yet another set of protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Structural and functional constraints in the evolution of protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Polymerase chain reaction primers miss half of rRNA microbial diversity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Biopython: freely available Python tools for computational molecular biology and bioinformatics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

A simple, fast, and accurate method of phylogenomic inference

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

MetaSim: a sequencing simulator for genomics and metagenomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Rubellimicrobium mesophilum sp. nov., a mesophilic, pigmented bacterium isolated from soil

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Metagenomics: read length matters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Orthologous transcription factors in bacteria have different functions and regulate different genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Evidence for a gram-positive, eubacterial root of the tree of life

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

MEGAN analysis of metagenomic data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Improving the specificity of high-throughput ortholog prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

6 July 2018

The PROSITE database.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

6 July 2018

The metagenomics of soil

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

MUSCLE: multiple sequence alignment with high accuracy and high throughput

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Local homology recognition and distance measures in linear time using compressed amino acid alphabets

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

The Pfam protein families database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

BLAT—The BLAST-Like Alignment Tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

EMBOSS: the European Molecular Biology Open Software Suite

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Codon-substitution models for heterogeneous selection pressure at amino acid sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Uprooting the tree of life

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

3D domain swapping: a mechanism for oligomer assembly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Crotonobetaine reductase from Escherichia coli--a new inducible enzyme of anaerobic metabolization of L(-)-carnitine.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

Basic local alignment search tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3772700

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1756-0500-5-460

Systematic artifacts in metagenomes from complex microbial communities.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1756-0500-5-460

Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1756-0500-5-460

Modeling residue usage in aligned protein sequences via maximum likelihood

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22925230

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1756-0500-5-460

1 reference

Dimensions Publication ID

1 August 2017

0 references

1 reference

1 August 2017

1 reference