Plasmid Atlas

At the moment, pATLAS does not allow you to submit your reads or Fasta files to analyze in a remote server.

However, there exist two auxiliary scripts that can be run locally (i.e. on your local pc). Instructions are provided in their respective menus. For instance, if you want to check if a given sequence is related to plasmids present in pATLAS, you can go to 'Import', then 'Sequence'. If, on the other hand, you wish to know which plasmids are present in your reads, you can go to 'Import' and then you will have two options for that: 'Mapping results' and 'Mash screen'.

pATLAS just support JSON files, so you can use auxiliary scripts to generate these JSON file and then you can import then through 'Import' side menu.

pATLAS uses NCBI refseq database and therefore only plasmid sequences that are present in this database are represented in this network. Plasmids in other databases such as the 'nucleotide' or even European nucleotide archive may be absent from pATLAS.

However, You can open an Issue on github with the list of accession numbers of the plasmids you would like to see in pATLAS.

pATLAS uses NCBI RefSeq database and therefore despite our continuous efforts to avoid gene sequences, chromosomes and other sequences that are not plasmids, the manual curation of the ever growing RefSeq plasmid database is a daunting task. Therefore we acknowledge all contributions that can help "clean" our database.

To do so, you can open an Issue on github with the list of accession numbers of the sequences that you have found in pATLAS that do not correspond to plasmids and state the reason for such.

Note: To submit an issue you will need to have a GitHub account.

This means that the shared part of their sequences have at least 90% average nucleotide identity (mash distance of 0.1 or less).

On the one hand, this gives an idea of the modularity of some components that compose plasmids, i.e., some small modules can be very easily integrated by larger plasmids. On the other hand, this may be odd when looking for similar plasmids and thus we implemented an option that allows to filter these differences in sequence size between pairs of plasmids. This option can be accessed through the left side menu, by selecting 'size ratio'.

You can share your results by exporting a project using the sidebar menu. Just go to Projects -> Export and save your project.

Then send the file to your co-workers.

You can save your current session by saving a Project. Just go to Projects -> Export and save your project.

Then, when you come back to pATLAS, just load this new file through sidebar menu Project -> Import option. Select a 'view' and you are good to go.

Make sure that your browser is not blocking popups, because pATLAS will attempt to open a new window do make the download request to the database.