Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering (Q31152170)

15 August 2017

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

1 reference

15 August 2017

1 reference

Weizhong Li

0 references

Shibu Yooseph

0 references

Granger Sutton

1 reference

15 August 2017

10 April 2008

1 reference

15 August 2017

1 reference

15 August 2017

1 reference

15 August 2017

182

1 reference

PMC publication ID

2362130

Creative Commons Attribution 2.0 Generic

15 August 2017

start time

10 April 2008

1 reference

April 2022 Public Data File from Crossref

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

Unravelling the ORFan Puzzle

1 reference

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Quantitative assessment of protein function prediction from metagenomics shotgun sequences

21 June 2018

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Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

21 June 2018

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

21 June 2018

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

21 June 2018

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CAMERA: a community resource for metagenomics

21 June 2018

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

21 June 2018

1 reference

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Accurate phylogenetic classification of variable-length DNA fragments

21 June 2018

1 reference

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Database resources of the National Center for Biotechnology Information

21 June 2018

1 reference

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MetaGene: prokaryotic gene finding from environmental genome shotgun 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=2362130

Metagenomic analysis of the human distal gut 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=2362130

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=2362130

Community genomics among stratified microbial assemblages in the ocean's interior

21 June 2018

1 reference

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21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Bioinformatics for whole-genome shotgun sequencing of microbial communities

21 June 2018

1 reference

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Genome Streamlining in a Cosmopolitan Oceanic Bacterium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Genome sequencing in microfabricated high-density picolitre reactors

21 June 2018

1 reference

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Microbial community genomics in the ocean

21 June 2018

1 reference

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Comparative metagenomics of microbial communities

21 June 2018

1 reference

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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=2362130

Environmental genome shotgun sequencing of the Sargasso Sea

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Community structure and metabolism through reconstruction of microbial genomes from the environment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

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=2362130

The TIGRFAMs database 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=2362130

Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Clustering of highly homologous sequences to reduce the size of large protein databases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Comparison of sequence profiles. Strategies for structural predictions using sequence information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

The TIGR gene indices: reconstruction and representation of expressed gene 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=2362130

Finding families for genomic ORFans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Heuristic approach to deriving models for gene finding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

The ProDom database of protein domain 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=2362130

PAML: a program package for phylogenetic analysis by 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=2362130

CATH--a hierarchic classification of protein domain structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

SCOP: a structural classification of proteins database for the investigation of sequences and structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

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=2362130

DNA sequencing with chain-terminating 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=2362130

Finding novel genes in bacterial communities isolated from the environment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Scaling law in sizes of protein sequence families: from super-families to orphan genes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Tolerating some redundancy significantly speeds up clustering of large protein databases

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2362130

Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18402669

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-9-182

1 reference

journals/bmcbi/YoosephLS08

15 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

PMC publication ID

2362130

15 August 2017

PubMed publication ID

18402669

1 reference

PMC publication ID

2362130