MicroScope: a platform for microbial genome annotation and comparative genomics

Salzberg, 2007, Genome re-annotation: a wiki solution?, Genome Biol., 8, 102, 10.1186/gb-2007-8-1-102

Lima, 2009, HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot, Nucleic Acids Res., 37, D471, 10.1093/nar/gkn661

Klimke, 2009, The National Center for Biotechnology Information's; Protein Clusters Database, Nucleic Acids Res., 37, D216, 10.1093/nar/gkn734

Overbeek, 2005, The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes, Nucleic Acids Res., 33, 5691, 10.1093/nar/gki866

Markowitz, 2008, The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions, Nucleic Acids Res., 36, D528, 10.1093/nar/gkm846

D'A;scenzo, 2004, PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences, Nucleic Acids Res., 32, 3124, 10.1093/nar/gkh615

Winsor, 2005, Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation, Nucleic Acids Res., 33, D338, 10.1093/nar/gki047

Glasner, 2006, ASAP: a resource for annotating, curating, comparing, and disseminating genomic data, Nucleic Acids Res., 34, D41, 10.1093/nar/gkj164

Hubbard, 2009, Ensembl 2009, Nucleic Acids Res., 37, D690, 10.1093/nar/gkn828

Overbeek, 2003, The ERGO genome analysis and discovery system, Nucleic Acids Res., 31, 164, 10.1093/nar/gkg148

Walter, 2009, PEDANT covers all complete RefSeq genomes, Nucleic Acids Res., 37, D408, 10.1093/nar/gkn749

Meyer, 2003, GenDB – an open source genome annotation system for prokaryote genomes, Nucleic Acids Res., 31, 2187, 10.1093/nar/gkg312

Almeida, 2004, A system for automated bacterial (genome) integrated annotation – SABIA, Bioinformatics, 20, 2832, 10.1093/bioinformatics/bth273

Bryson, 2006, AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system, Nucleic Acids Res., 34, 3533, 10.1093/nar/gkl471

Pellegrini, 1999, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc. Natl Acad. Sci. USA, 96, 4285, 10.1073/pnas.96.8.4285

Overbeek, 1999, Use of contiguity on the chromosome to predict functional coupling, In Silico Biol., 1, 93

Marcotte, 1999, Detecting protein function and protein-protein interactions from genome sequences, Science, 285, 751, 10.1126/science.285.5428.751

Markowitz, 2009, IMG ER: a system for microbial genome annotation expert review and curation, Bioinformatics, 25, 2271, 10.1093/bioinformatics/btp393

Vallenet, 2006, MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Res., 34, 53, 10.1093/nar/gkj406

Barbe, 2004, Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium, Nucleic Acids Res., 32, 5766, 10.1093/nar/gkh910

Bairoch, 2009, The Universal Protein Resource (UniProt) 2009

Pruitt, 2007, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, D61, 10.1093/nar/gkl842

Bairoch, 2000, The ENZYME database in 2000, Nucleic Acids Res., 28, 304, 10.1093/nar/28.1.304

Bocs, 2003, AMIGene: Annotation of MIcrobial Genes, Nucleic Acids Res., 31, 3723, 10.1093/nar/gkg590

Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.955

Lagesen, 2007, RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 35, 3100, 10.1093/nar/gkm160

Gardner, 2009, Rfam: updates to the RNA families database, Nucleic Acids Res., 37, D136, 10.1093/nar/gkn766

Cruveiller, 2005, MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes, Nucleic Acids Res., 33, W471, 10.1093/nar/gki498

Tatusov, 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41, 10.1186/1471-2105-4-41

Hunter, 2009, InterPro: the integrative protein signature database, Nucleic Acids Res., 37, D211, 10.1093/nar/gkn785

Claudel-Renard, 2003, Enzyme-specific profiles for genome annotation: PRIAM, Nucleic Acids Res., 31, 6633, 10.1093/nar/gkg847

Sonnhammer, 1998, A hidden Markov model for predicting transmembrane helices in protein sequences, Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175

Bendtsen, 2004, Improved prediction of signal peptides: SignalP 3.0, J. Mol. Biol., 340, 783, 10.1016/j.jmb.2004.05.028

Gardy, 2005, PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics, 21, 617, 10.1093/bioinformatics/bti057

Karp, 2002, The Pathway Tools software, Bioinformatics, 18, S225, 10.1093/bioinformatics/18.suppl_1.S225

Waterhouse, 2009, Jalview Version 2—a multiple sequence alignment editor and analysis workbench, Bioinformatics, 25, 1189, 10.1093/bioinformatics/btp033

Kanehisa, 2008, KEGG for linking genomes to life and the environment, Nucleic Acids Res, 36, D480, 10.1093/nar/gkm882

Hacker, 2001, Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes, EMBO Rep., 2, 376, 10.1093/embo-reports/kve097

Caspi, 2008, The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Res., 36, D623, 10.1093/nar/gkm900

Serres, 2000, MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products, Microb. Comp. Genomics, 5, 205, 10.1089/mcg.2000.5.205

Selengut, 2007, TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes, Nucleic Acids Res., 35, D260, 10.1093/nar/gkl1043

Gil, 2004, Determination of the core of a minimal bacterial gene set, Microbiol. Mol. Biol. Rev., 68, 518, 10.1128/MMBR.68.3.518-537.2004

Carver, 2008, Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, 24, 2672, 10.1093/bioinformatics/btn529

Sayers, 2009, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 37, D5, 10.1093/nar/gkn741

Matsumoto, 1978, Chromosomal location of genes participating in the degradation of purines in Pseudomonas aeruginosa, Mol. Gen. Genet., 167, 165, 10.1007/BF00266910

Pelletier, 2008, ‘Candidatus Cloacamonas acidaminovorans’: genome sequence reconstruction provides a first glimpse of a new bacterial division, J. Bacteriol., 190, 2572, 10.1128/JB.01248-07

Saier, 2006, TCDB: the Transporter Classification Database for membrane transport protein analyses and information, Nucleic Acids Res., 34, D181, 10.1093/nar/gkj001