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Genomic Tools

Provides general statistical data about a replicon, such as: Length, GC%, Ribosomal RNAs, tRNAs types, Annotations Status, Average CDS length, Repeated regions, Average intergenic length , Protein coding density, Scaffolds/Contigs numbers, etc.
CGView is a Java package which allows to produce high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a mean of generating visual output suitable for the web. Starting with information of one genome and the features to visualize, CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format) and completes it with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views (More Information).
Reference: Stothard P, Wishart DS. «Circular genome visualization and exploration using CGView.» Bioinformatics. 2005 Feb 15 ;21(4):537-9
This functionalty provides the list of Genomic regions containg tandem duplications of protein coding genes. Tandem duplicated genes have an identity ≥ 35% with a minLRap ≥ 0.8 and are separated by a maximum of 5 consecutive genes.
This tool computes the statistic distribution of the protein coding genes of the selected genome within the COG (Clusters of Orthologous Groups; cf. «A genomic perspective on protein families», Tatusov et al., 1997) functional categories. These values are computed using the automatic results obtained with the COGNiTOR software (http://www.ncbi.nlm.nih.gov/COG/).
Minimal Gene Set includes well conserved housekeeping genes for basic metabolism and macromolecular synthesis, many of which are essential genes (the list of these genes is taken from Gil R, Silva FJ, Peretó J, «Moya A. Determination of the core of a minimal bacterial gene set.» Microbiol Mol Biol Rev. 2004 Sep ;68(3):518-37).
To find the homologs, the tool analyses the similarity results between the genes of each organism and the set of 206 genes from 7 genomes (Escherichia coli K12, Bacillus subtilis 168, Candidatus Blochmania floridanus, Buchnera aphidicola APS, Buchnera aphidicola Bp, Buchnera aphidicola Sg and Mycoplasma genitalium G37).
The candidate genes have to fill one of the 2 following conditions :
  • share a BBH relationship with a minLRap > 0.5
  • belong to a synteny group
E. coli has numerous representatives of genes present in the oldest living ancestor genome as deduced by these methods. The minimal set of genes obtained is a function of which and how many genomes are chosen for the analysis. As more E. coli genomes are completed, the Common Core will be more defined.
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