How to use

General information

TopoIBase is a database where you can consult informations about topoisomerases IA and their distribution into taxa and families. Some well known comparison tools are available to help you to go futher in your studies.

This site is organized with pages displaying informations for each element, like topoisomerases (example), families (example), and taxa (example).
You can use the search bar at the top right of the screen to look for any element (topoisomerase, family, taxon) referenced in the database. You can search by typing a protein sequence (complete or not), an ID (uniprot, genbank, topoDB) or a name.
Once you submitted your request, a summary of found results is displayed. Here, you can view the results in a condensed form (click "Show") or a more detailled form (click "Details"). The latter shows the found elements with some more informations.
The browse menu (in the navigation bar) allows you to select families or taxa by navigating in a global view of the families tree and taxa tree respectively. You can click to expand children, and double-click to access this element's informations.
The advanced search let you chose a combination of queries for more complex requests. First, choose what you want to find. You can add or remove forms by clicking on "Add a search box" and "Remove this search box" respectively. For each search box, you can choose between various forms.

On each page displaying a topoisomerase or a group of topoisomerase, you can use a set of tools on them. These tools are generally available on the topoisomerases pages, taxa or families pages, detailled search results page, and on the selection page. These tools are also available without direct input, in the navigation bar. For direct inputs, you can add your proteins in fasta format to the text area, then choose your parameters and run the tool by clicking the "Submit" button. Please refer to each particular tool page for more informations.
You can download selected data. The available formats are fasta and tsv.
BLAST (Basic Local Alignment Search Tool) will perform a comparison between each of the entries and the chosen protein sequences bank.
Multiple alignment
MUSCLE (MUltiple Sequence Comparison by Log-Expectation) is a multiple alignment tool. It produces a multiple alignment between at least two entries.
VLD is an alignment-free classification tool. It provides a clustering based on the comparison of your inputs.

A selection is a custom set of topoisomerases which you can chose to group together and thus access to various informations on this set. There is a total of 3 selections available. You can see your selections by clicking "My Selection".
Add topoismerase(s) to a selection
There are two ways to add topoisomerases to a selection :
  • By clicking "Add to selection" and chosing the selection on a given element's page (this option on a family or taxon page will add all topoisomerases of this family or taxon to the selection).
  • By using the menu "My Selection > Upload to selection". In this page you can add a set of uniprot IDs, genbank IDs or taxa names, manually or with a file upload. The corresponding topoisomerases will be automatically added to the chosen selection.
Selection content
Access to informations on your selection(s) by clicking "My Selection" in the navigation bar. You can delete all the topoisomerases in your selection by clicking on the "Clear" button. You can delete one topoisomerase of your selection by clicking the "Delete" button in the corresponding row.