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

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 geospiza.com) 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"

Questions from our mailbag: How do I cite FinchTV?

One of the questions that appears in our mailbox from time to time concerns citing FinchTV or other Geospiza products. A quick search with Google Scholar for "FinchTV" finds 42 examples where FinchTV was cited in research publications. Most of the citations seem to follow the same conventions.

We recommend citing FinchTV as you would any other experimental software tool, instrument, or reagent. The citation should include the version of the program, the company, the location, and the web site. Other Geospiza products (FinchLab, Finch Suite, and iFinch) may be cited in similar manner.

In our case, a citation would most likely read:

FinchTV 1.4.0 (Geospiza, Inc.; Seattle, WA, USA; http://www.geospiza.com)

If you're not sure which version of FinchTV you're using, open the About menu. The version number will appear on the page.

It would also be a good idea to check with the journal where you plan to submit the article. Most journals have a set of instructions for authors where they provide example citations.

Entering information in iFinch via FinchTV, part I

Teaching is a hard habit to break so I teach short courses now and then.

This year, I've been having my students use FinchTV to enter their blast results into iFinch. This also works with FinchLab and other Finch systems, too.

This has been pretty helpful. The data get stored for each chromatogram and we can all view the results (I'll address this part in a later post.)

How does this work?

1. Log in to your Finch account. Open a chromatogram in FinchTV either by clicking the FinchTV icon or the link from the Chromat Read page that says Open in FinchTV.

2. When you're ready to enter information, click the Commit button (outlined below).



3. You'll see a message appear asking if you're sure. Say "yes."

4. Enter the information that you want to store. Since we were using FinchTV to connect to NCBI blast and identify our bacteria, I'm entering the conclusion from my blast results.

5. Then I click the "OK" button.



6. If I refresh my web browser page, I can see that the version number for my read is now at "2", and I can see that my information has been stored in the database.



In a later post, I'll show how we get that information out.

Stay tuned...

iFinch in education: metagenomics with JHU, part I.

iFinch is the perfect bioinformatics tool to accompany a class. I used it Fall quarter in a class that I teach at Shoreline Community College (Washington) and I'm using it right now in an on-line class that I teach at Austin Community College (Texas).

We cover several different topics in the class, but I have a fondness for long projects where we can use multiple techniques and tie everything to a common theme.

This semester we're working with bacterial sequences that were obtained from students at John Hopkins University. I've been collaborating with an instructor there for several years and now we have four years of data to dig our teeth into.

This video describes the first part of the project that we're working on.



JHU bacterial metagenomics project from Sandra Porter on Vimeo.

Capturing your images from FinchTV: PCs with Windows

As many of you know, FinchTV is wonderful tool for viewing and editing the trace files from your chromatograms.

Naturally, many people would like to be able to generate images from FinchTV for publications and talks.

In this post, I'm going to describe how to capture your images from FinchTV if you're using a PC with Windows. In the next post, I'll write about capturing images on Macs.


If you're using a PC with Windows

1. Open some kind of program for storing the image - this could be any image editing program or even a program like Microsoft Word.


2. Open FinchTV and find the part of the trace that you want to capture.


3. Hold the shift key down, then press the Ctrl key, and the PrintScrn key. This will capture whichever window is active. Since you were just working with FinchTV, you should have captured the FinchTV window.


4. Open a new document in Word, PowerPoint, or whatever image program you're using.


5. Click the Ctrl key and the V key to paste the image in the document.


6. Edit as necessary.

Addendum: I've also been told that Snagit is another really nice screen capture program for PCs.