NCBI prokaryotic genome annotation pipeline

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes

(2013) J. Zhou et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Database resources for the tuberculosis community

(2013) Jocelyne M. Lew et al.   TUBERCULOSIS

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

(2012) Pablo Pareja-Tobes et al.   PLoS One

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Solving the Problem: Genome Annotation Standards before the Data Deluge

(2011) William Klimke et al.   Standards in Genomic Sciences

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Using comparative genome analysis to identify problems in annotated microbial genomes

(2010) M. S. Poptsova et al.   MICROBIOLOGY-SGM

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

(2010) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The National Center for Biotechnology Information's Protein Clusters Database

(2008) William Klimke et al.   NUCLEIC ACIDS RESEARCH

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation

(2008) Samuel V. Angiuoli et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY