Plasmid Atlas is a web interface that allow
browse plasmid sequences available in the NCBI refseq
database. Here you can obtain metadata related with the
available plasmid sequences, such as species in which
they were described, antibiotic resistance information
and much more.
We are always happy
to improve user experience, so if you
please report them to us. You can also contact us in
Note: pATLAS was tested for Google
Chrome, Firefox, Safari and Microsoft Edge, however
we recommend using Google Chrome
for a better experience.
pATLAS is a web-based tool enabling searching for a
specific plasmid (or plasmids) of interest, visualize the
available plasmid database and to identify plasmids
contained in High Throughput Sequencing data.
FCT - "Fundação para a Ciência e a Tecnologia"and
[FCT/ Scientific and
Technological Research Council of Turkey (Türkiye Bilimsel
ve Teknolojik Araşrrma Kurumu, TÜBİTAK)]
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 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.
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'.