MaGe (Magnifying Genomes)
Genome Browser interface provides an user-friendly way to visualize and explore a replicon content (cartographic map of the genome), together with the similarity results (synteny maps) obtained with other bacterial genomes available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). Artemis tool can be launched at this level to examine more precisely the nucleotidic/proteic sequences (a useful interface to correct translational start codon positions if necessary). For genomic objects drawn in part of the chromosome visualized in the cartographic map, additional information is listed in a table.
This tool allows the user to change his/her settings of the various interfaces proposed in the MicroScope platform: hide or show the tool descriptions, change genome and synteny map size, selection of specific genomes for the synteny maps, etc.
Provides a list of genes which share identical gene names in a same replicon.
This tool computes the list of CDSs which ovelap, in their 5' extremity, with the following CDS. Sorted by the length of the overlaps (in bp), this list is useful to remove artefactual CDS (false positive) and/or to correct translational start codon position.
This tool provides a general overview of the expert annotations perform on protein genes for the selected genome, mainly the number of validated CDSs, and their distribution in Product Type and Cellular Localization categories (Riley M «Functions of the gene products of Escherichia coli.» Microbiol Rev. 1993 Dec;57(4):862-952. ) and Evidence Classes (inspired from http://www.pseudomonas.com/). These statistics does not include the automatic functional annotations.
EC number Update( Not available for guests )
Only available for users having an account, i.e working on a MicroScope project with the LABGeM team. This interface lists the EC numbers given by the user during the process of expert annotation which are not still valid within the ENZYME resource.
Annotation Mapping( Not available for guests )
Only available for users having an account. Provides CDS label (i.e, locus_tag) correspondences between a new version of the genome being annotated/analysed (progression of the sequencing step) and the old one(s).