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Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

Figure 1

Overview of Gegenees.

The Gegenees workspace contains one or several local databases. Genomes can be downloaded from the NCBI ftp site or from custom ftp sites through a built-in ftp client. This client compares the content of the local database with the remote one and highlights genomes already present locally. Unpublished genomes or genomes downloaded from other sources can be imported. The Gegenees workspace can also contain comparison projects. Genomes are added to the comparison from the local database. Genomes already in the active comparison are highlighted in the local database to facilitate the update process. Comparisons can also be downloaded from www.gegenees.org or shared between labs and imported into the workspace. One or several fragmented alignments can be made in the comparison with custom-specified resolution. Large alignments are associated with lengthy calculations and can therefore be paused and later resumed. Genomes can also later be added to a completed alignment that is then updated with the missing data points. When an alignment has been completed, the phylogenomic context can be analyzed in heat-plots. Nexus files can be exported for dendrogram construction and heat plots can be exported for high-resolution printouts. The alignment can then be analyzed in terms of Biomarker scores and uniqueness signatures. A target and a background group are defined on the basis of strain phenotypes and phylogenomic overview. The resulting conservation pattern signature can then be viewed and explored graphically or in tables. The signatures can also be exported to Artemis. Primers and/or probes can be designed from the signatures and candidate primers can be added back to Gegenees in form of a primer/probe alignment. Primer specificity can then be analyzed in terms of mismatches in the target and background groups.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0039107.g001