The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data (Q33815258)

29 July 2017

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data (English)

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29 July 2017

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Shibu Yooseph

12

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Tanja M Davidsen

8

object named as

Tanja Davidsen

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29 July 2017

7

Ramana Madupu

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29 July 2017

5

Nikhat Zafar

1 reference

29 July 2017

6

Mathangi Thiagarajan

1 reference

29 July 2017

David M Tanenbaum

1

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29 July 2017

Johannes Goll

2

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29 July 2017

Sean Murphy

3

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29 July 2017

Prateek Kumar

4

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29 July 2017

Leonid Kagan

9

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29 July 2017

Saul Kravitz

10

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29 July 2017

Douglas B Rusch

11

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29 July 2017

30 March 2010

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Standards in genomic sciences

29 July 2017

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29 July 2017

2

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29 July 2017

2

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29 July 2017

229-237

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https://scigraph.springernature.com/pub.10.4056/sigs.651139

29 July 2017

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cites work

The comprehensive microbial resource

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Annotation of metagenome short reads using proxygenes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

MEGAN analysis of metagenomic data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

An experimental metagenome data management and analysis system

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Using pyrosequencing to shed light on deep mine microbial ecology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Bioinformatics for whole-genome shotgun sequencing of microbial communities

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Environmental genome shotgun sequencing of the Sargasso Sea

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

The Pfam protein families database

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Enzyme-specific profiles for genome annotation: PRIAM

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

The COG database: an updated version includes eukaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

The TIGRFAMs database of protein families

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Gene ontology: tool for the unification of biology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Profile hidden Markov models

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

A hidden Markov model for predicting transmembrane helices in protein sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Base-calling of automated sequencer traces using phred. II. Error probabilities

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Functions of the gene products of Escherichia coli.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Microbial ecology and evolution: a ribosomal RNA approach

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Basic local alignment search tool

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3035284

Performance evaluation of amino acid substitution matrices

4 July 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21304707

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.4056/SIGS.651139

1 reference

Dimensions Publication ID

29 July 2017

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29 July 2017

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