Bioinformatics for biotech students: my favorite computer programs

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Sandra Porter

The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses.

Why not use the Web?
Before going on, I should probably explain, why we use desktop programs, we have so many things available on the web. We do use the web whenever we can. Web services are nice because you can shift the computation burden to someone else's computer. (I think this perfectly fair in most cases, since we've paid for many of these with our tax dollars.) However, sometimes, the desktop versions are much nicer than the versions that you can run through web services. JalView (www.jalview.org) is much nicer as a desktop program than the version we can run through the Embl web server. Some programs, like FinchTV, only run on desktop computers. And then there is the problem of speed and predictability. If you're at work and a network is unbearably slow, you might find something else to do. If you're teaching a class, with a limited time, it can be excruciatingly painful to have all of your students wait for an unpredictable amounts of time for their results.

My favorite desktop programs
1. A web browser I like Firefox because of it's ability to search for text and highlight all instances of that text in a noticable color. Plus, there are links at the NCBI web site that don't work in Safari.

2. Adobe Acrobat Reader We can't read pdf documents without it, and I have to use pdf documents because other file types behave in too many different ways with different web browsers.

3. FinchTV - We use FinchTV to look at trace files and learn about data quality (or lack thereof). Examples are here and here. Plus it's free and runs on most kinds of computers (Windows, Mac, Linux).

4. JalView We use JalView for viewing multiple alignments of DNA or protein sequences. The alignments themselves are created in either Clustal or Muscle - you can either open the aligned sequences in JalView or load the sequences and then, if you're on the Internet, select the option to generate the alignment.

The only downside of using JalView is that the documentation isn't complete (in my opinion). For example, if we use the option to generate alignments with Clustal, we don't get any information about the parameters that were used for this step. We don't know if the right matrix was used, etc. So - that part is typical, but it isn't good.

You can see some examples of JalView in action here and here.

5. Cn3D. My favorite structure-viewing program. You can do so much more with Cn3D than you can from using web-plug-ins.

6. Microsoft Word and Excel. Believe it or not, I used Word to help assemble a DNA sequence, several years ago. For people who are never going to need or want to program, Word is nice and easy. You can search for strings of text, count characters, work with text, etc. And lots of bioinformatics activities involve those kinds of things, just on a larger scale.

Plus, students can take notes in Word and e-mail the notes to themselves at the end of class.

We use Excel to sort, count, calculate, and graph. Again, it's simple and familiar, and for an introductory course, or people who are never going to need to program, it works just fine.

7. NJ plot - this is a really nice application for viewing and working with phylogenetic trees.

8. Sometimes we also use the Phylip package of programs from Joe Felsenstein at the University of Washington.

Notice - I'm not listing programs like blast since we often run that at the NCBI.


What your favorite desktop programs for teaching with bioinformatics?