4.6 Article

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A. Schaffer et al.

BMC BIOINFORMATICS (2020)

Article Biochemical Research Methods

VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening

Alejandro A. Schaffer et al.

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

25 years of serving the community with ribosomal RNA gene reference databases and tools

Frank Oliver Gloeckner et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Genetics & Heredity

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences

Pablo Yarza et al.

MARINE GENOMICS (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

Alexey M. Kozlov et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Ribosomal Database Project: data and tools for high throughput rRNA analysis

James R. Cole et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

Kenan Hadziavdic et al.

PLOS ONE (2014)

Article Biochemical Research Methods

nhmmer: DNA homology search with profile HMMs

Travis J. Wheeler et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biotechnology & Applied Microbiology

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

Kuan-Liang Liu et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

Article Biochemical Research Methods

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

Elmar Pruesse et al.

BIOINFORMATICS (2012)

Article Multidisciplinary Sciences

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Conrad L. Schoch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Jan Pawlowski et al.

PLOS BIOLOGY (2012)

Article Evolutionary Biology

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

Jonas Zimmermann et al.

ORGANISMS DIVERSITY & EVOLUTION (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Review Biotechnology & Applied Microbiology

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

Dominik Begerow et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Local RNA structure alignment with incomplete sequence

Diana L. Kolbe et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

RNAmmer:: consistent and rapid annotation of ribosomal RNA genes

Karin Lagesen et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

ARB:: a software environment for sequence data

W Ludwig et al.

NUCLEIC ACIDS RESEARCH (2004)