Profile hidden Markov models for the detection of viruses within metagenomic sequence data (Q30843773)

13 October 2017

Profile hidden Markov models for the detection of viruses within metagenomic sequence data (English)

1 reference

13 October 2017

1 reference

1

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13 October 2017

3

Katherine S Pollard

1 reference

13 October 2017

Thomas J Sharpton

2

1 reference

PMCID

4139300

13 October 2017

Joseph L DeRisi

series ordinal

4

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PMCID

4139300

13 October 2017

language of work or name

English

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publication date

20 August 2014

1 reference

13 October 2017

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13 October 2017

9

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13 October 2017

e105067

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13 October 2017

8

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Creative Commons Attribution 4.0 International

13 October 2017

start time

20 August 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

PRICE: software for the targeted assembly of components of (Meta) genomic sequence data

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Next-generation sequencing technology in clinical virology

21 June 2018

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Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

21 June 2018

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Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease

21 June 2018

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Application of next-generation sequencing technologies in virology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Virus identification in unknown tropical febrile illness cases using deep sequencing

21 June 2018

1 reference

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Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia

21 June 2018

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Mimivirus shows dramatic genome reduction after intraamoebal culture

21 June 2018

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HMMER web server: interactive sequence similarity searching

21 June 2018

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Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

21 June 2018

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Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua

21 June 2018

1 reference

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A new generation of homology search tools based on probabilistic inference

21 June 2018

1 reference

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The Pfam protein families database

21 June 2018

1 reference

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 June 2018

1 reference

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NCBI Reference Sequences: current status, policy and new initiatives

21 June 2018

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Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent

21 June 2018

1 reference

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Emerging Pathogens: Challenges and Successes of Molecular Diagnostics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Global trends in emerging infectious diseases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

The Pfam protein families database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Protein homology detection by HMM-HMM comparison

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Genome sequence of a polydnavirus: insights into symbiotic virus evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

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=4139300

Viral Discovery and Sequence Recovery Using DNA Microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

A comparison of profile hidden Markov model procedures for remote homology detection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

BLAT—The BLAST-Like Alignment Tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

An efficient algorithm for large-scale detection of protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Establishment of an infectious RNA transcription system for Striped jack nervous necrosis virus, the type species of the betanodaviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Profile hidden Markov 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=4139300

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

A conserved family of cellular genes related to the baculovirus iap gene and encoding apoptosis inhibitors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Identification of the herpes simplex virus type 1 gene encoding the dUTPase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Improved tools for biological sequence comparison

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Identification and separation of the two subunits of the herpes simplex virus ribonucleotide reductase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

The complete genome of klassevirus - a novel picornavirus in pediatric stool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Temporal trends in the discovery of human viruses.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

From RNA to DNA, why so many ribonucleotide reductases?

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139300

Molecular identification of novel viruses

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25140992

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0105067

1 reference

13 October 2017

0 references

1 reference

13 October 2017

1 reference

PMCID

4139300