The Xdom 2.0 documentation


What is xdom ?

Xdom is an X-window application which may visualize the output of the script mkdom2, thus helping you to achieve a systematic analysis of the modular organisation of any set of protein sequences.
With this program, you may execute different queries to retrieve all or part of your proteins. The tool displays the proteins as a set of boxes; each box represents a domain, Those boxes are clickable, leading to a popup menu, from which you may start a new query, or display the whole family this domain belongs to.
The protein name is also clickable, which gives you the opportunity to execute still other queries, or to display the protein sequence.
You may also print part or all of your query.

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Running xdom

You may run xdom with the following commands:

xdom &
xdom project.prj &

The second form starts xdom and opens a new project file.

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The Project menu

 

For full functionality, xdom needs 3 files, with the extensions srs, xdom, fasta:

As it is fastidious to open 3 files everytime xdom is launched, we save in a file, with extension .prj the names of those 3 files. This file is called a project file.

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Create a New Project

Use this option to create a new project. Only the field labelled Xdom File is required, however it is obviously better filling also the Project Name field, as the windows of the application are entitled with this name. You must also fill the other two fields to benefit from all the functionalities.

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Save a Project

Use this option to save the project (ie the name and up to 3 data files, as previously discussed) inside a new project file.

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Open a project

Use this option to open a project previously saved. It is also possible to start the application with the project file specified on the command line, in which case the project is automatically opened. Besides, the mkdom2pp.pl script creates a project file, which can be opened by the xdom program.

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Open a new window

Use this option to open a new window, which will use the same data as the first window. This is convenient to display simultaneously different parts of the file.

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The query menu

You may ask the program for some queries, in order to display all or part of the protein set.

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Undo/Redo

During an Xdom session, you'll ask for several queries one after. The queries are stored in a stack, so that you may Undo or redo them as necessary during the session.

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All Proteins

Use this option to display all the proteins. When a project is opened, xdom executes this query. However, it is sometimes convenient executing again this request during a work session.

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Select Proteins

Use this option to ask for a query, giving a protein name as parameter. You have several ways for selecting a protein to query for:

  1. If you known its name, type its name inside the Fiter field.
  2. If you don't know exactly its name, type only some characters in the Filter field, then press the button Filter: only the matching proteins are then displayed in the scrolled list, so that it is much more easier to select the protein you are interested in.
  3. You may also just scroll the list, then click on your protein when it appears in the list. This can be a rather fastidious process, however, when there are many proteins in the set.

You may also use one the the radio buttons labelled View option to choose between several options:

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Select Domains

Use this option to ask for a query, giving one or several domain names as parameters. You may fill 3 fields for building the query:

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An alternative way of selecting a domain

A click with the right button of the mouse when the cursor is on a domain box will open a popup menu with the option of displaying all proteins which include domain 34. This is quite equivalent to click the Query/Select Domains option, and fill only the AND field, querying only domain nb. 34.


The view menu

Find Protein

With this option, you can select a protein to find among the displayed proteins: you may type the name of the protein, or select its name in the list (this list shows only the names of the displayed proteins), or even type a part of its name, then click the FILTER button to restrict the listes protein names. When found, the protein name is displayed in blue (next figure).

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Find again

If you just found a protein, and you lost it because you scrolled the window or because you executed another request, you may find it again with this option. Should the protein not returned by the current request, an error message will be produced. If no protein was selected using the Find option, the Find again option is inactive.

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Cancel find

This options makes inactive the find again button, thus resetting the Find protein action.

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Graphical or textual representations

A protein domain is always represented as a clickable rectangular box; however, the box may be labelled with different ways:

The last representation should be in theory the best one, however it is sometimes difficult to distinguish between 2 neibouring colors, when there are as more as 64 color levels. This could lead to some interpretation errors, so that it is sometimes convenient switching between those many representations.

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An alternative way of selecting a color mode

The color mode may be selected from the command line, as follows:

 
  xdom --color 64

Sort by alphabetical order

Use this option to alphabetically sort the displayed proteins, using their names as a sort key.

Sort by architecture

Use this option to sort the displayed proteins, using their architecture as a sort key. This is a very convenient option, as it puts together the proteins which share the same architecture.

What is an architecture ?

The architecture is defined as the domains composition of the protein. For example, if a protein is composed with domains 76, 34,76, 100, 76 the architecture is the 34-76-76-76-100 string.

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The sort algorithm

For sorting the proteins by architecture, the following algorithm is executed:

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Complete/simplified output

When the displayed proteins are sorted by architecture, on can switch between those two options:

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The popup menus

You may call several functionalities, clicking with the left-button or the right-button of the mouse, when the pointer is located on two sorts of areas:

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The protein popup menus

This menu is displayed when you click a protein name with the right button.

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The domain popup menus

This menu is displayed when you click a protein name with the right button.

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Citing the xdom2 program

Should you use this program for a publication, please cite the following reference: Gouzy J., Eugene P., Greene E.A., Kahn D., Corpet F. (1997).\n XDOM, a graphical tool to analyse domain arrangements in protein families., Comp. Appl. BioSci. The release 2 of xdom is a complete rewrite of the software, but the main functionalities, as described in this paper, were kept unchanged.

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The authors of the xdom2 program

The release 2 of xdom was written by:

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at L.I.P.M. (I.N.R.A.-C.N.R.S.), in the research group managed by Daniel Kahn. This work was partially founded by Genopole