Friday, May 21, 2010

I Want My FinchTV*

Without a doubt FinchTV is a wildly successful sequence trace viewer. Since it’s launch, close to 150,000 researchers and students have enjoyed its easy to use interface, cross platform capabilities, and unique features. But, where does it go from here? 

Time for Version 2

FinchTV is Geospiza's free DNA sequence trace viewer that is used on Macintosh, Windows, and Linux computers to open and view DNA sequence data from Sanger-based instruments. It reads both AB1 and SCF files and displays the DNA sequence and four color traces of the corresponding electropherogram. When quality values are present, they are displayed with the data. Files can be opened with a simple drag and drop action, and once opened, traces can be viewed in a either a single pane or multi-pane full sequence format. Sequences can be searched using regular expressions, edited, and regions selected and used to launch NCBI BLAST searches.

Over the past years we have learned that FinchTV is used in many kinds of environments suchas research labs, biotechnology and pharmaceutical companies, and educational settings. In some labs, it is the only tool people use to work with their data. We’ve also collected a large number of feature requests that include viewing protein translations, performing simple alignments, working with multiple sequences, changing the colors of the electropherogram tracings, and many others.

Free software is not built from free development 

FinchTV was originally developed under an SBIR grant as a prototype for cross platform software development. Until then, commercial quality trace viewers ran on either Windows or Macintosh, never both. Cross platform viewers were crippled versions of commercial programs, and none of the programs incorporated modern GUI (graphical user interface) features and were cumbersome to use.

FinchTV is a high quality, full featured, free program; we want to improve the current version and keep it free. So, the question becomes how to keep a free product up to date?

One way is through grant funding. Geospiza believes a strong case can be made to develop a new version of FinchTV under an SBIR grant because we know Sanger sequencing is still very active. From the press coverage, one would think next generation DNA sequencing (NGS) is going to be the way all sequencing will soon be done. True there are many projects where Sanger is no longer appropriate, but NGS cannot do small things, like confirm clones. Sanger sequencing also continues to grow in the classroom, hence tools like FinchTV are great as education resources. 

We think there are more uses too, so we’d like to hear your stories.

How do you use FinchTV?
What would you like FinchTV to do?

Send us a note (info at or, even better, add a comment below. We plan to submit the proposal in early August and look forward to hearing your ideas.

* apologies to Dire Straights "Money for Nothing"


Conrad Halling said...

At my job, we use Sequencher, a commercial product available for both Windows and Mac OS X, for viewing trace file data and performing assemblies. ApE (A Plasmid Editor) also runs on multiple platforms and can be used for viewing trace file data. I will try FinchTV, too.

Todd Smith said...

Thanks Conrad,

I checked out ApE. It has some nice features, but it is not a full featured for working with a trace file. Sequencher is similar in that respect. Hope you like FinchTV.