PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

(2014) Samuel M. D. Seaver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Enabling comparative modeling of closely related genomes: example genus Brucella

(2014) José P. Faria et al.   3 Biotech

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence

(2013) A. R. Wattam et al.   JOURNAL OF BACTERIOLOGY

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

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

In search of genome annotation consistency: solid gene clusters and how to use them

(2013) James J. Davis et al.   3 Biotech

Real Time Metagenomics: Using k-mers to annotate metagenomes

(2012) Robert A. Edwards et al.   BIOINFORMATICS

Genome Sequences of the Primary Endosymbiont “Candidatus Portiera aleyrodidarum” in the Whitefly Bemisia tabaci B and Q Biotypes

(2012) Zi-Feng Jiang et al.   JOURNAL OF BACTERIOLOGY

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

(2011) Khalid Mahmood et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

(2011) Mihail R. Halachev et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Selection of representative protein data sets

(2010) Uwe Hobohm et al.   PROTEIN SCIENCE

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Database resources of the National Center for Biotechnology Information

(2009) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS