[Fink-users] DNA sequence viewer

[David Orlovich]

Hello Fink users.

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. Specifically, what I need is an alternative to proprietary software like Genecodes' Sequencher or ABI's AutoAssembler. There are freeware programs like ABI's Editview, that allow the visualisation of single electropherograms, but I'm been unable to find free software that will allow the user to assemble and edit contiguous sequences (contigs). Typically, most users of DNA sequencers would sequence forward and reverse strands and then assemble the strands to form a consensus sequence, which is then cut and pasted into a text file in FASTA format for subsequent processing (multiple alignment etc).

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. 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 software - 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.

Any thoughts, suggestions, comments?

Cheers, David Orlovich.



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