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* This workshop was adapted from a more extensive EMBOSS Tutorial. Interested students may wish to go there to extend their skill set.

In the past few classes, you’ve learned a few things about sequence analysis. You’ve come to understand how to find data at NCBI. In addition you have learned about some theory that underlies sequence alignments. Today you will learn about using a set of tools available at many research institutions including UMDNJ, the EMBOSS Suite.

The EMBOSS software suite is available for many different platforms including Unix, Linux, Mac OS X, and Windows. A web interface for EMBOSS known as EMBOSS Explorer is light-weight and easy to use.

EMBOSS integrates a lot of bioinformatics packages and tools for sequence analysis into a single environment. It can use data in a variety of formats and even can retrieve sequence data from the web. The libraries that individual EMBOSS programs use are also provided with the package, making it a platform in which scientists can develop and release software in the Open Source traditions. EMBOSS provides more than just competition to other commercial packages; in some ways, it exceeds in performance.

Scientists who regularly use these applications or recursively use one or more of the applications in research will find it productive to work within the UNIX shell interface to EMBOSS. That kind of work is beyond the scope of this workshop. If you are interesed you can find more information at

http://emboss.sourceforge.net/developers/acd/commandline.html

The web interface to the EMBOSS suite at UMDNJ EMBOSS-Explorer is available at http://emboss.umdnj.edu/emboss.

Note: This link will open in a new browser window or a new tab, depending on your browser settings. We suggest you consider adopting a web browser that supports tabbed windows such as Mozilla Firefox or later editions of Internet Explorer. These browsers allow you to view multiple web pages within one window. We find it easier to navigate keeping one tab on this tutorial, and another on EMBOSS instead of having multiple browser windows. But the good news is that EMBOSS Expolrer is quite browser-neutral, so the choice is yours.

You will see two panes. The left pane contains a list of all the applications available in EMBOSS. The right pane shows the information pertaining to the current application you want to run. To search for a particular application, look in the left pane, or use the program wossname to find what you are looking for. Scroll down the left pane and located wossname, then click on it. It is located under the heading "Information".

You should now see information in the right-pane pertaining to wossname. Click on "Run wossname". You will now get a list of all available programs (same as the left-pane) plus a description of each program.

Some interesting things to point out:

Within each application, you can choose to have the results of the application emailed to you. This can be useful for applications that will take a long time to run.

At the top of each application is a link to "read the manual". The manual contains a lot of useful information about the program. If at any time you have questions as to how to use the application, or how to interpret the output, the first place to look is the manual.

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Page last modified September 29, 2008