I am pleased to announce that a new version of SeqTrace, my free and open source software for viewing and processing Sanger DNA sequencing trace files, is now available. It had been nearly two years since the 0.8.1 release of SeqTrace, and over the Christmas break I decided it was finally time to get a new release finished up and out the door. So I want on a major coding binge and now, many hours of work later, SeqTrace 0.9.0 is done (actually, it was done a few days ago!).
SeqTrace 0.9.0 includes many new features and improvements in comparison to 0.8.1 as well as a few bug fixes. Some of the most important upgrades include full support for all IUPAC nucleotide codes, a new algorithm for computing consensus sequences from matched forward and reverse traces that is based on Bayesian statistical methods, the ability to search for PCR primers in the trace sequences and display the primers along with the sequence data, an algorithm for trimming primers (and trailing bases) from consensus sequences, and synchronized scrolling of matched forward and reverse traces. This latter feature is a big improvement when navigating paired forward and reverse sequencing traces, at least in my opinion. There are many other improvements, too, which you can read about in SeqTrace's release history.
I want to thank the users of SeqTrace who took the time to send me feedback and suggestions regarding the previous version of the software. Your comments were very helpful in deciding what to focus on for 0.9.0!
Hi Brian,
ReplyDeleteThanks for writing such a cool little program that is free and open source. I'm currently having trouble with manually editing my sequence files. After importing them and grouping them I can't edit the sequences manually. The icons are all greyed out (copy/delete/edit). Is there an option somewhere I'm missing?
Auto trim has been disabled, I'm currently on an XP machine at work. Here's a screenshot:
http://i.imgur.com/QsJWSfv.png
Hi, Ammar,
DeleteThanks, and I'm glad that SeqTrace is useful for you! To edit the sequence, you need to first use the mouse to select the bases you want to edit from the working sequence (this is the bottom-most sequence in the image you attached), and then copy/edit/delete should all work. See item 8 in the documentation page for more information: http://code.google.com/p/seqtrace/wiki/TraceViewWindow.
I hope that helps!
-Brian
Dear Brian,
ReplyDeleteThank you for developing such nice program and for making it freely available. I would only say that it would be nice if in the consensus (working) sequence one could edit an ambiguity naming it Y, M, R, etc, instead of the uninformative N.
Best wishes,
Tiago