Browse
The Browse functions allow the user to explore the plasmid database. pATLAS uses a curated version of refseq plasmid database from NCBI and establishes the relationships between all plasmids available in the database through MASH by estimating the pairwise distances between all plasmids. For a more detailed explanation on how are these relationships handled and displayed refer to Relationships and distances estimations
Table Of Contents
Browse
Distances
Distances are represented in pATLAS as grey links between nodes (dark grey circles). This options allows the user to display how closely related are a group of plasmids or a plasmid with another plasmid. It has three color schemes options: blue, green and red. You may choose which one you see fit using a simple dropdown menu.
The darker the color, the smaller is the distance estimated by MASH and thus the more closely related (more similar) are the two linked nodes.
Length
You may filter by lenght of the plasmids present in the database. To do so, select the By Length option under the Browse submenu, which will open a smaller window above the visualization. Then, you may use both the slider and the boxes for minimum and maximum limits, which will change the selected plasmids. Dark grey plasmids are within the current interval whereas lighter grey plasmids are outside the interval.
Size ratio
This option allows users to filter links that have plasmids with very different sizes. E.g. some plasmids may have a high mash dist (> 0.9) but one of the plasmids may be a lot smaller than the other. This ratio allows to specify a percentage between the smaller and the larger plasmid, connected by a link:
Size Ratio = 1 - (smaller plasmid length / larger plasmid length)
The cutoff that the user should provide is the maximum percentage difference between the two plasmids. So, if we set it to 30 this will tell pATLAS to highlight or remove all the connections that have more than 30% difference in size between pairs of plasmids.
Shared sequence
This option allow to filter links between plasmids that, despite having a small mash distance (< 0.1, i.e., very similar plasmids in some portion of their sequence), present only a fraction of each other in terms of sequence alignment. Although we call this module "Shared sequence", this in fact uses the percentage of hashes generated by mash dist that are shared between pairs of sequences and thus associated with each link.
Taxa
In this option you may select a multitude of taxa filters ranging from order to species. This will highlight with different colors each of the selected taxa. For instance, if you select Acinetobacter in the genus dropdown, the plasmids in which the host genus was Acinetobacter will be highlighted.
Annotation
Plasmid families
This option allows users to color plasmids present in pATLAS by selecting genes available in PlasmidFinder database. A dropdown menu with all genes present in this database is available for the user to select, and searches are enabled with a live filter of resulting genes.
Citation:
[Carattoli, A., Zankari, E., García-Fernández, A.,
Larsen, M. V., Lund, O., Villa, L., Aarestrup, F. M., Hasman, H.
(2014). In Silico detection and typing of plasmids using plasmidfinder and
plasmid multilocus sequence typing. Antimicrobial Agents and Chemotherapy,
58(7), 3895–3903.](https://doi.org/10.1128/AAC.02412-14).
Resistances
Two resistance genes databases (CARD and Resfinder) are available in pATLAS and it's possible to highlight plasmids that contain the resistance genes selected by the user.
Citations:
[Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M.,
Rasmussen, S., Lund, O., Aarestrup, F. M., Larsen, M. V. (2012).
Identification of acquired antimicrobial resistance genes. Journal of
Antimicrobial Chemotherapy, 67(11), 2640–2644.](https://doi.org/10.1093/jac/dks261)
[Jia, B., Raphenya, A. R., Alcock, B., Waglechner, N., Guo, P.,
Tsang, K. K., Lago B. A., Dave B. M., Pereira S., Sharma A. N.,
Doshi S., Courtot M., Lo R., Williams L. E., Frye J. G., Elsayegh T.,
Sardar D., Westman E. L., Pawlowski A. C., Johnson T. A.,
Brinkman F. S., Wright G. D.,
McArthur, A. G. (2017). CARD 2017: Expansion and
model-centric curation of the comprehensive antibiotic resistance
database. Nucleic Acids Research, 45(D1), D566–D573.](https://doi.org/10.1093/nar/gkw1004)
Virulence
The user can highlight plasmids containing virulence genes available in VFDB database.
Citation:
[Chen L, Yang J, Yu J, et al. VFDB: A reference database for
bacterial virulence factors. Nucleic Acids Res. 2005;33(DATABASE ISS.)
:D325-D328. doi:10.1093/nar/gki008.](https://academic.oup.com/nar/article/33/suppl_1/D325/2505203)
Advanced
It is possible to browse pATLAS through a combination of filters.
Multiple
In this menu allows the users to combine different filters between each of the available levels:
Taxa,
Plasmid Families,
Resistances,
Virulence.
It is allowed to select multiple entries in one of the dropdown menus for each level. For instance, you can select Straphyloccocus OR Enterococcus from the genera filter. The selection made within each filter level will behave as a sum of the selected entries. However, if you select a filter from another level, for example, VanA gene from the CARD filter, pATLAS selection will behave as an intersection or union of the filters, depending on which of the following buttons is clicked:
The Submit intersection will make an intersection between two taxa levels.
In the example above, the resulting visualization will highlight the plasmids that share in common the selected Taxa AND the selected resistance, marked in purple.
The Submit union will make an union between each one of the filter levels.
In the example above, the taxa and resistance selections will be combined and displayed as a single color.
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