The integrated microbial genomes system: an expanding comparative analysis resource

We review below integrated microbial genomes 's data content and analysis tool extensions since the last published report on IMG

Victor M. Markowitz; I-Min A. Chen; Krishna Palaniappan; Ken Chu; Ernest Szeto; Yuri Grechkin; Anna Ratner; Iain Anderson; Athanasios Lykidis; Konstantinos Mavromatis; Natalia N. Ivanova; Nikos C. Kyrpides

2009

Scholarcy highlights

  • The integrated microbial genomes system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context
  • Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases
  • IMG records its primary genome sequence information from RefSeq including its organization into chromosomal replicons and scaffolds and/or contigs, together with predicted protein-coding sequences, some RNA-coding genes and protein product names that are provided by the genome sequence centers
  • Every genome included in IMG is associated with metadata attributes, available from GOLD
  • We review below IMG's data content and analysis tool extensions since the last published report on IMG
  • The metabolic capabilities of genomes can be analyzed using functional profile tools applied on enzymes together with a tool for finding ‘missing’ enzyme that are marked by a null abundance in the function profile result. Such a null abundance for an specific ‘missing’ enzyme leads to the ‘Find Candidate Genes for Missing Function’ tool, as illustrated in Figure 4(iv), which allows users to search for candidate genes that could be associated with this missing enzyme either via KEGG Ortholog terms or homolog/ortholog genes associated with it
  • The result of the search for candidate genes, illustrated in Figure 4(v), consists of a list of genes that can be selected and included into the ‘Gene Cart’ and further examined using various tools, such as gene neighbourhood analysis and multiple sequence alignment tools

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