The IMG/M data management and analysis system v.7: content updates and new features

Origin and Evolution of Nitrogen Fixation in Prokaryotes

(2022) Hong-Wei Pi et al.   MOLECULAR BIOLOGY AND EVOLUTION

DOE JGI Metagenome Workflow

(2021) Alicia Clum et al.   mSystems

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

CATH: expanding the horizons of structure-based functional annotations for genome sequences

(2018) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

(2018) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

(2016) Michalis Hadjithomas et al.   NUCLEIC ACIDS RESEARCH

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

InCHlib – interactive cluster heatmap for web applications

(2014) Ctibor Škuta et al.   Journal of Cheminformatics

Infernal 1.1: 100-fold faster RNA homology searches

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

TIGRFAMs and Genome Properties in 2013

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

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Evidence for Nitrogen Fixation by "Dehalococcoides ethenogenes" Strain 195

(2009) P. K. H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS