IMG/M 4 version of the integrated metagenome comparative analysis system

IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M’s data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M’s database architecture, annotation and data integration pipelines and analysis tools have been extended to copewith the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp).

[1]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[2]  Natalia Ivanova,et al.  A call for standardized classification of metagenome projects. , 2010, Environmental microbiology.

[3]  I-Min A. Chen,et al.  IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project , 2012, PloS one.

[4]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[5]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[6]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[7]  I-Min A. Chen,et al.  The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..

[8]  T. Takagi,et al.  MetaGene: prokaryotic gene finding from environmental genome shotgun sequences , 2006, Nucleic acids research.

[9]  Nikos Kyrpides,et al.  CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats , 2007, BMC Bioinformatics.

[10]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[11]  I-Min A. Chen,et al.  IMG/M: the integrated metagenome data management and comparative analysis system , 2012, Nucleic Acids Res..

[12]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[13]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[14]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[15]  M. Borodovsky,et al.  Ab initio gene identification in metagenomic sequences , 2010, Nucleic acids research.

[16]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[17]  I-Min A. Chen,et al.  IMG 4 version of the integrated microbial genomes comparative analysis system , 2013, Nucleic Acids Res..

[18]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[19]  Robert C. Edgar,et al.  PILER-CR: Fast and accurate identification of CRISPR repeats , 2007, BMC Bioinformatics.

[20]  Haixu Tang,et al.  FragGeneScan: predicting genes in short and error-prone reads , 2010, Nucleic acids research.

[21]  Alejandro A. Schäffer,et al.  A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences , 2006, J. Comput. Biol..

[22]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[23]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .