The automatic annotation of bacterial genomes
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[1] M. Metzker. Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.
[2] Claudine Médigue,et al. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. , 2002, Microbiology.
[3] Paul Stothard,et al. Automated bacterial genome analysis and annotation. , 2006, Current opinion in microbiology.
[4] W. Pearson. Rapid and sensitive sequence comparison with FASTP and FASTA. , 1990, Methods in enzymology.
[5] J Hacker,et al. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution , 1997, Molecular microbiology.
[6] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[7] Rachael P. Huntley,et al. The GOA database in 2009—an integrated Gene Ontology Annotation resource , 2008, Nucleic Acids Res..
[8] Huaiqiu Zhu,et al. Genome reannotation of Escherichia coli CFT073 with new insights into virulence , 2009, BMC Genomics.
[9] Amos Bairoch,et al. PROSITE, a protein domain database for functional characterization and annotation , 2009, Nucleic Acids Res..
[10] Jaques Reifman,et al. AGeS: A Software System for Microbial Genome Sequence Annotation , 2011, PloS one.
[11] Nikos Kyrpides,et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats , 2007, BMC Bioinformatics.
[12] Steven Salzberg,et al. A probabilistic method for identifying start codons in bacterial genomes , 2001, Bioinform..
[13] R. Overbeek,et al. The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[14] Jenn-Kang Hwang,et al. Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions , 2004, Protein science : a publication of the Protein Society.
[15] Christoph Dehio,et al. Signature-tagged mutagenesis: technical advances in a negative selection method for virulence gene identification. , 2005, Current opinion in microbiology.
[16] S. Salzberg,et al. Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.
[17] Deborah Hix,et al. PATRIC: The VBI PathoSystems Resource Integration Center , 2006, Nucleic Acids Res..
[18] Terri K. Attwood,et al. PRINTS and its automatic supplement, prePRINTS , 2003, Nucleic Acids Res..
[19] Jaques Reifman,et al. The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation , 2008, BMC Bioinformatics.
[20] Kenneth E. Rudd,et al. Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map , 1998, Microbiology and Molecular Biology Reviews.
[21] E. Koonin. Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.
[22] Andrew C. Stewart,et al. DIYA: a bacterial annotation pipeline for any genomics lab , 2009, Bioinform..
[23] C. Médigue,et al. MaGe: a microbial genome annotation system supported by synteny results , 2006, Nucleic acids research.
[24] Martin Ester,et al. Sequence analysis PSORTb v . 2 . 0 : Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis , 2004 .
[25] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[26] Alan J. Cann. Genomes , 2012, Principles of Molecular Virology.
[27] R. Barrangou,et al. CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.
[28] J. Gardy,et al. Methods for predicting bacterial protein subcellular localization , 2006, Nature Reviews Microbiology.
[29] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[30] E. Koonin. Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .
[31] Jonathan D. G. Jones,et al. Application of 'next-generation' sequencing technologies to microbial genetics , 2009, Nature Reviews Microbiology.
[32] María Martín,et al. Ongoing and future developments at the Universal Protein Resource , 2010, Nucleic Acids Res..
[33] Duane Szafron,et al. BASys: a web server for automated bacterial genome annotation , 2005, Nucleic Acids Res..
[34] Fiona S. L. Brinkman,et al. Evaluation of genomic island predictors using a comparative genomics approach , 2008, BMC Bioinformatics.
[35] Christos A. Ouzounis,et al. Genome coverage, literally speaking , 2005 .
[36] Sarah A Teichmann,et al. Relative rates of gene fusion and fission in multi-domain proteins. , 2005, Trends in genetics : TIG.
[37] Rick L. Stevens,et al. The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.
[38] Zhiyong Lu,et al. Predicting subcellular localization of proteins using machine-learned classifiers , 2004, Bioinform..
[39] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[40] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[41] Tibor Vellai,et al. Distribution and evolution of short tandem repeats in closely related bacterial genomes. , 2008, Gene.
[42] Leon Goldovsky,et al. Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. , 2005, EMBO reports.
[43] Claudine Médigue,et al. MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes , 2005, Nucleic Acids Res..
[44] Hampapathalu A. Nagarajaram,et al. MICdb: database of prokaryotic microsatellites , 2003, Nucleic Acids Res..
[45] Steven J. M. Jones,et al. IslandPath: aiding detection of genomic islands in prokaryotes , 2003, Bioinform..
[46] Erik L. L. Sonnhammer,et al. Domain architecture conservation in orthologs , 2011, BMC Bioinformatics.
[47] Julian Parkhill,et al. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence , 2007, BMC Genomics.
[48] S. Salzberg,et al. Prediction of transcription terminators in bacterial genomes. , 2000, Journal of molecular biology.
[49] C. Ouzounis,et al. Percolation of annotation errors through hierarchically structured protein sequence databases. , 2005, Mathematical biosciences.
[50] Carsten Damm,et al. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models , 2006, BMC Bioinformatics.
[51] Kiejung Park,et al. WeGAS: A Web-Based Microbial Genome Annotation System , 2009, Bioscience, biotechnology, and biochemistry.
[52] Robert D. Finn,et al. DUFs: families in search of function , 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.
[53] Zhirong Sun,et al. Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..
[54] Ibtissem Grissa,et al. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..
[55] J. Do,et al. Computational approaches to gene prediction. , 2006, Journal of microbiology.
[56] N. Mulder,et al. InterPro and InterProScan: tools for protein sequence classification and comparison. , 2007, Methods in molecular biology.
[57] Mikhail S. Gelfand,et al. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes , 1998, German Conference on Bioinformatics.
[58] Wing-Kin Sung,et al. Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines , 2005, BMC Bioinformatics.
[59] Arcady R. Mushegian,et al. Computational methods for Gene Orthology inference , 2011, Briefings Bioinform..
[60] Erik L. L. Sonnhammer,et al. PfamAlyzer: domain-centric homology search , 2007, Bioinform..
[61] Michael Watson,et al. ProGenExpress: Visualization of quantitative data on prokaryotic genomes , 2005, BMC Bioinformatics.
[62] Carole A. Goble,et al. BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..
[63] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[64] G. Olsen,et al. CRITICA: coding region identification tool invoking comparative analysis. , 1999, Molecular biology and evolution.
[65] Rolf Apweiler,et al. InterPro and InterProScan , 2007 .