Tuesday, May 8, 2012

FinchTV on Lion

Okay, it took a while, but FinchTV, Geospiza's popular Sanger sequencing trace viewer is now available on Mac OS X Lion.

While the same great features are still great, the underlying code has been updated to run the application as a native intel binary, so it can be great into the future.

Features make FinchTV cool

In addition to all the basic things you'd expect a trace viewer to do like open AB1 or SCF files, view bases, electropherogram peaks, quality values, and reverse complement sequences, and dynamically scale data, FinchTV also lets you edit bases, print traces, and view detailed information about your trace file.  And, you can open files with a simple drag and drop action, as you'd expect for a modern desktop application.

That's not all, there's more

What really makes FinchTV stand out, is the ability to view your trace in a single-pane or multi-pane view. The latter view is ideal for visualizing the full data contained in the trace. In multi-pane view you can even change the horizontal or vertical scales.

FinchTV also integrates with NCBI's BLAST services.  In the application you can highlight a region of sequence and either use the edit menu or right click with your mouse to get the BLAST menu to choose between nucleotide (BLASTn), translated nucleotide (BLASTx), translated nucleotide + translated database (TBLASTx), or mega BLAST options.

Less obvious features include the ability to search for sub sequences in your DNA sequence and observe the raw data for a trace. Subsequence searching uses Perl style regular expressions and a Greedy algorithm so you can enter a search term and, each time you hit return, the next best match is identified including subsequences within subsequences. For example, the regular expression - ATG((?!TAG|TAA|TGA)...)+(TAG|TAA|TGA) - will find open reading frames. If one reading frame is contained within another, the longer reading frame is found first.

Another less known feature is the raw data view.  The raw data view is essential for those work with sequencing instruments.  Many do not realize the standard electropherogram trace image is processed data. That is, a mathematical matrix computation is applied to normalize signals, subtract background fluorescence, and correct natural mobility shifts in the data. The result is an easy to interpret view of the data. However, if you need to troubleshoot your sequencer and see the real details you'll want to view the rawest data possible. FinchTV is the only available trace viewer, outside of ABI's software that provides this capability.

To obtain FinchTV please visit http://www.geospiza.com/Products/finchtv.shtml