Bioinformatics Using wEMBOSS


Introduction

EMBOSS (European Molecular Biology Open Source Software) can perform sequence alignment (local and global), automatically transform different data formats, get retrieval sequences from your local computer or database or the web, find motifs and enzyme sites, and use drawing tools. wEMBOSS is a web interface to most but not all EMBOSS programs.

The software is available to the School of Biomolecular and Physical Sciences, Griffith University University students, faculty, and staff and this document provides information about accessing wEMBOSSS at Griffith

 

Account setup for wEMBOSS

For your class, you will be provided with a unique user name and password so that you can use wEMBOSS. You will be required to use these to login into wEMBOSS, so please do remember them.

 

Accessing and using wEMBOSS

1. Go to: http://trishul.sci.gu.edu.au/wEMBOSS

2. Log in with your valid IU Network ID.

3. To start a new project, click New project at the top of the project management page and give the project a name. The project here is similar to a file folder you might use to organize your papers. For example, say you have two projects ongoing, one about the mutation of mitochondria and the other about the recombination rate of mitochondria. You can either create two projects, "mutation" and "recombination", or put them in one project "mitochondria" and have subprojects "mutation" and "recombination" within that one project.

4. On the project management page, choose a program by its function or from the alphabetical list on the left. The program page will replace the project management page, but the command list on the left side will remain, so that you can easily switch to other functions.

5. Upload your data and set up options if necessary, and then click the Run button on the program page to run the program. The result will be displayed in a new window.

6. You can save your results on your local computer if you wish. All files generated are kept on the Discern server and will still be available when you log in again. Files generated by wEMBOSS that are older than 180 days will be automatically removed to free up space.

7. To see the manual, click the Manual button at the upper right. A new window will open to show you the manual.

8. You will be provided details instructions during lectures in the computer labs. The following reference pages will used as part of these instructions.

 

: Project Management


FUNCTION

Create, rename, move and delete projects.

Manage outputs of programs that where executed inside the active project.

Operate on project files: create a new file, view, edit, copy (rename) and delete files, import GCG lists, upload files from your PC

 DESCRIPTION

Projects

A new user is invited to create a first project.  

The user space available for navigation is limited to all the projects created by the user underneath a user directory namedwProjects.

It's a good practice to create projects with names relevant for the user job.

A project may be divided in subprojects, subprojects may also be divided with unlimited depth.

A project and all of its contain may be renamed or moved to become a  subproject of another one, a subproject

may also be moved  higher  in the projects tree.

The user selects the active project or subproject with the selector located on the wEMBOSS header.

Programs are always executed in the active project.

To avoid annoying repeated operations, its highly recommended to write in the nucList and protList files of you current project, the EMBOSS USA names or sequence filenames of the most pertinent sequences for the project.

Lists produced by SRS, blast, seqinfo ... can easely be introduced in nucList and protList, making all included sequences available with a click for any program!

Remember that with such a philosophy you can create an environment where you always retrieve in the project of interest the sequences of interest!

Project Results 

Outputs of programs are saved in individual directories under the project where there were executed.

By default, results are ordered by date, the last one being on the top, to get it immediately.


If you have a lot of results, to find an old one (e. g. a blast result) is very easy: sort by name and look to the date, the secondary key is the date!

Some outputs serve as input data for other programs: you can always copy outputs in the current project or any other project, click on the "files" button of a result to make the copy facility available (see "Files" item)

Files 

Files are sequence files, lists of sequence names, data and specific management files for which the names are starting with a dot.

Some experience is needed to avoid accumulation of outputs and files in the same project, making a mess:  don't hesitate to divide your projects in subprojects!

 

USAGE

Frame

To create a new project click on the "New project" button and enter the name of the project in the Message Box that appears.

To create a subproject of exercices-day2 project (e.g. comparisons), the active project must be "exercices-day2", click on the "subproject" checkbox then click on the "New project" button.

To  active project  can be moved  to any other location  in  the projects tree  using the "Move proj. to"  button.

To delete a project it must be the active one, the one of which the name appears above the project management frame (Confirmation is asked!)

Frame

<>Contains links to the outputs of the programs executed in the current project (e.g.dotmatcher 05.02.16  11.50.54: means an http link to the output results of dotmatcher executed the 16 of February  2005 at 11.50.54 pm)

By clicking on the Files button you activate the "copy facility"  to copy the output file(s) of your program in any of the projects.

<>You can also delete obsolete or inadequate results by selecting  some  or all  of those  by clicking  on  the checkboxes  (the upper one  select/unselect  all  the results ) . Once your click  on the "Del selection"  button,  a confirmation box appear  asking for trully delete  the selected results.

Frame

 

In each project or subproject, 2 files are automatically created : "nucList" and "protList", edit these files to write there the names of your favourites nucleic and proteic sequences concerning the project. (Lists produced by SRS, blast, seqinfo are welcome, copy and paste the lists in nucList or protList)

The sequences names can be names of files located in the active project or database sequence names, using EMBOSS USA.

To view a file, select the filename in the selector and click on the "View" button.

To edit a file, select the filename in the selector and click on the "Edit" button.

To copy (a) file(s) select the filename(s) and click the "Copy" button. You will have to select the project in which you will paste the files.

To rename a file, select the filename and click on the "Copy" button. You will have to select the project in which you will paste it and to enter in a textbox the new name of the file.

To delete (a) file(s) select the filename(s) and click on the "Delete" button. You have to confirm your decision. 

To create a new file, click on the "New File" button. This is the recommended way to get sequences from your personal computer by copy and paste.

To convert GCG list files to a compatible format for EMBOSS and GCG, select the list and click on the "list G->E&G" button.

Some types of files can be viewed using applets (multiple alignments with Jalview, phylogenetics trees with ATV) , this will be developed in the future.

To upload a file from your local computer, first browse for the file on your PC and then click on the "Upload" button.


Comments and suggestions to:Professor Bharat Patel <b.patel@griffith.edu.au>
HTML'd by Bharat Patel
[Created: 11 February 2008]
[Updated: 24 February 2008]