David Orlovich wrote:
I'm writing to ask if anyone knows of open source software available for MacOS/X11 that allows the user to view, manipulate and edit electropherograms from an ABI DNA sequencer.I'm a bit out of the loop, having spent the last 4 years getting into web design instead of doing molecular biology, but from what I can see such a freeware progam doesn't currently exist.
I've had a bit of a look at some packages available through Fink, notably Emboss, but this doesn't do what I've described above.Well, Emboss does do multiple alignments, and it does allow you to edit them using Jemboss. And it also can display the ABI trace. It may not be a slick interface but you could manually display the trace and then look at your alignment. This is pretty much what I was doing last I did any sequencing, using ABI Seqed, older and quite poor ABI software but it was the best available to me.
Any help would be much appreciated. I think there would be an overwhelming demand for such an open source program since most of the downstream processing can be done for free by quite good softwareAt the moment it seems Emboss/Jemboss is the best bet, maybe you need to talk to the people building it, submit a feature request, whatever. It seems to me they could easily add the functionality you need, a button/script combination in the Jemboss multiple sequence editor that opened up the requisit ABI trace in abiview would be a good start.
I just can't believe that people without access to commercial software resort to editing electropherograms by hand from printouts of the ABI files to get the sequences in the first place.Well, for many people the time the spend learning to use the software is better spent just getting the job done (in their view). Given the pace of change in these technologies they're probably right, the next time they come to do it it'll be new software. Plenty of people will also have access to comercial software ABI, GCG (doesn't GCG do what you're asking these days?) etc. This was always the case in the university labs I studied/worked in.
It's not so long since we were moving a ruler down an autoradiogram, pencilling in the sequence on graph paper and then *typing it into the computer by hand* - The horror! The horror!
Arrggghhh, I'm too young to be making comments like that.
Good luck,
Adrian
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