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)]
ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI -
“Fundos Europeus Estruturais e de Investimento” from “Programa
Operacional Regional Lisboa 2020”.
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'.