- Home
- Publications
- Publication Search
- Publication Details
Title
Reference databases for taxonomic assignment in metagenomics
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume 13, Issue 6, Pages 682-695
Publisher
Oxford University Press (OUP)
Online
2012-07-12
DOI
10.1093/bib/bbs036
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
- (2011) Kuan-Liang Liu et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- UCHIME improves sensitivity and speed of chimera detection
- (2011) Robert C. Edgar et al. BIOINFORMATICS
- Flexible taxonomic assignment of ambiguous sequencing reads
- (2011) José C Clemente et al. BMC BIOINFORMATICS
- Analysis of 16S rRNA environmental sequences using MEGAN
- (2011) Suparna Mitra et al. BMC GENOMICS
- Computational challenges of sequence classification in microbiomic data
- (2011) P. Ribeca et al. BRIEFINGS IN BIOINFORMATICS
- Metagenomic Analysis of Brain Abscesses Identifies Specific Bacterial Associations
- (2011) M. Al Masalma et al. CLINICAL INFECTIOUS DISEASES
- On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys
- (2011) Patricio Jeraldo et al. ENVIRONMENTAL MICROBIOLOGY
- Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
- (2011) Thomas M. Gihring et al. ENVIRONMENTAL MICROBIOLOGY
- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
- (2011) B. J. Haas et al. GENOME RESEARCH
- Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
- (2011) O.-S. Kim et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- The sequence read archive: explosive growth of sequencing data
- (2011) Y. Kodama et al. NUCLEIC ACIDS RESEARCH
- GenBank
- (2011) D. A. Benson et al. NUCLEIC ACIDS RESEARCH
- The International Nucleotide Sequence Database Collaboration
- (2011) I. Karsch-Mizrachi et al. NUCLEIC ACIDS RESEARCH
- The NCBI Taxonomy database
- (2011) S. Federhen NUCLEIC ACIDS RESEARCH
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants
- (2011) Mariam Susan LaTuga et al. PLoS One
- Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks
- (2011) Giovanna Carpi et al. PLoS One
- Release LTPs104 of the All-Species Living Tree
- (2011) Raúl Munoz et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Experimental factors affecting PCR-based estimates of microbial species richness and evenness
- (2010) Anna Engelbrektson et al. ISME Journal
- Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
- (2010) Minseok Kim et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Quantifying microbial communities with 454 pyrosequencing: does read abundance count?
- (2010) ANTHONY S. AMEND et al. MOLECULAR ECOLOGY
- The European Nucleotide Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton
- (2010) M. L. Cuvelier et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses
- (2010) Pablo Yarza et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
- (2010) T. Chen et al. Database-The Journal of Biological Databases and Curation
- The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
- (2010) Patrick D. Schloss PLoS Computational Biology
- Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals
- (2010) Mahmoud A. Ghannoum et al. PLoS Pathogens
- Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys
- (2009) N. Youssef et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Metagenomics: Concept, methodology, ecological inference and recent advances
- (2009) Jagtar Singh et al. Biotechnology Journal
- The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
- (2009) Rolf Henrik Nilsson et al. FEMS MICROBIOLOGY LETTERS
- Polymerase chain reaction primers miss half of rRNA microbial diversity
- (2009) SunHee Hong et al. ISME Journal
- 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
- (2009) M. Buée et al. NEW PHYTOLOGIST
- Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere
- (2009) A. Jumpponen et al. NEW PHYTOLOGIST
- The ITS2 Database III—sequences and structures for phylogeny
- (2009) Christian Koetschan et al. NUCLEIC ACIDS RESEARCH
- A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes
- (2009) Linda A. Amaral-Zettler et al. PLoS One
- Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies
- (2009) Yong Wang et al. PLoS One
- BioJava: an open-source framework for bioinformatics
- (2008) R. C. G. Holland et al. BIOINFORMATICS
- 5.8S-28S rRNA interaction and HMM-based ITS2 annotation
- (2008) Alexander Keller et al. GENE
- A Bioinformatician's Guide to Metagenomics
- (2008) V. Kunin et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
- (2008) Z. Liu et al. NUCLEIC ACIDS RESEARCH
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- (2008) J. R. Cole et al. NUCLEIC ACIDS RESEARCH
- The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
- (2008) Pablo Yarza et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
- (2008) Susan M. Huse et al. PLoS Genetics
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now