# Browse

The Browse functions allow the user to explore the plasmid database. pATLAS uses a curated version of *refseq* plasmid database from [NCBI](ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/) and establishes the relationships between all plasmids available in the database through [MASH](http://mash.readthedocs.io/en/latest/) 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](/docs/api/distances.md)

**Table Of Contents**

* [Browse](browse.md:27#browse)
  * [Distances](/docs/usage/sidebar/browse.md#distances)
  * [Length](/docs/usage/sidebar/browse.md#length)
  * [Size ratio](/docs/usage/sidebar/browse.md#size-ratio)
  * [Taxa](/docs/usage/sidebar/browse.md#taxa)
* [Annotation](/docs/usage/sidebar/browse.md#annotation)
  * [Plasmid families](/docs/usage/sidebar/browse.md#plasmid-families)
  * [Resistances](/docs/usage/sidebar/browse.md#resistances)
  * [Virulence](/docs/usage/sidebar/browse.md#virulence)
* [Advanced](/docs/usage/sidebar/browse.md#advanced)
  * [Multiple](/docs/usage/sidebar/browse.md#multiple)

## 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.

![](https://github.com/tiagofilipe12/pATLAS/tree/70001e32d809856e7f793ffcebd527d812e7824e/docs/gitbook/images/distancedropdown.png)

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.

![](/files/-LJYLWRC9fpQl6R92HLf)

### 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.

![](/files/-LJYLWRE8iEf-IFCnJWI)

### 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.

![](/files/-LJYLWRGQ-DBxhGzZlwS)

## 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:

![](/files/-LJYLWRIF4zISX2A5D0W)

The `Submit intersection` will make an intersection between two taxa levels.

![Drawing](/files/-LJYLWRKtjp6YqAJuIft)

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.

![Drawing](/files/-LJYLWRMtRCYoA2N2nmT)

In the example above, the taxa and resistance selections will be combined and displayed as a single color.


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# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://patlas.gitbook.io/docs/usage/sidebar/browse.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.