This review provides pros and cons for three widely used DNA analysis programs. Two of these (Chromas and Finch TV) are simple viewing and editing applications. The third (MEGA) also allows for viewing and editing but “ups the ante” considerably in terms of power in DNA data analysis. In evaluating these applications, special consideration was given to how easily an imported DNA sequence could be viewed, edited and submitted to GenBank (http://www.psc.edu/general/software/packages/genbank/genbank.php) using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Instructors thinking of adding sequence analysis exercises to a course should also consider the ease with which a program can be used by undergraduates so the class maximizes the biology and minimizes time spent floundering with the intricacies of software. (A note to the reader: Upon opening a sequence file, the user views an electropherogram (or chromatogram): sequence data generated by automated sequencing. A discussion of cycle sequencing beforehand provides students with a sense of the method used to produce such data.)
Application #1: Chromas (http://www.technelysium.com.au/chromas.html)
The beauty of Chromas is its simplicity. Once a sequence file is opened, students edit the sequence by denoting and then deleting right and left cutoff regions that may contain poor sequence. Sequence editing in Chromas is intuitive and straightforward. After editing, the user chooses the BLAST option from the File menu and a GenBank database search commences. In my opinion, this is a great DNA editing application. Students can quickly move from manipulating raw sequence data to learning about BLAST and GenBank. Whereas other applications may be downloaded for free, Chromas offers a free 60-day trial, after which the program costs $69.
Pros: 60-day free trial; easy to use; efficient sequence editing Cons: $69 after trial period
Application #2: Finch TV (http://www.geospiza.com/Products/finchtv.shtml)
A nifty feature of Finch TV allows the user to drag a chromatogram onto the program to get started. Viewing, editing and proceeding to a BLAST search is straightforward, much like Chromas. A minor difference between the programs comes during a BLAST search. In Finch TV a BLAST search takes the user to a NCBI options page where search parameters must be defined. This can be tricky for a first-time user. Chromas allows the user to define these parameters beforehand (perhaps set by the instructor) and skip right to a database search. Overall, the differences between Chromas and Finch TV are small and Finch TV is a great choice.
Pros: Easy to use, free
Cons: BLAST search slightly more involved than with Chromas
Application #3: MEGA (http://www.megasoftware.net/)
MEGA bills itself as “evolutionary molecular genetic analysis” software and of the three applications reviewed, it is clearly the most powerful. MEGA allows the user to view, edit and search GenBank, just like FinchTV and Chromas. In addition, users can do a variety of other tasks such as align DNA sequences, construct phylogenetic trees, compute pairwise distances, consider molecular clocks and infer ancestral sequences. For the first-time user, there is a clickable button that takes you to useful sections entitled “A Walk Through MEGA” and “Evolutionary Analysis.” An appendix of frequently asked questions is also available. In addition, a tutorial button takes the user through program features complete with numerous examples. Overall, this program is a treasure-trove for DNA analysis and would fit nicely into a 400-level evolution course. While MEGA works for simple DNA editing and analysis, undergraduates and instructors may prefer a simpler analysis program.
Pros: Extremely powerful and varied DNA analysis; free
Cons: May be too complex for simple DNA editing exercises
In summary, all three applications are robust and extremely useful for DNA analysis in the classroom. Chromas and FinchTV have a lot of similarities and FinchTV has the edge with its free cost. MEGA is a far more powerful tool, recommended for more advanced students doing classroom or research projects.