Editview alternative

Joe Forrester joef at dnacore.mbp.missouri.edu
Tue Sep 5 07:18:16 EST 2000


Check out the following.

http://www.codoncode.com/TraceViewer/docs/Readme.htm

Joe Forrester
DNA Core Facility
University of Missouri

James Bonfield wrote:

> In <8ooomc$sai$1 at mercury.hgmp.mrc.ac.uk> Sven Klages <klages at molgen.mpg.de> writes:
>
> > Since we were just testing the machine I just have a few files.
> > But scf_dump gave me something like this ...
>
> > [Header]
> > 779314022       # magic_number
> > 20001           # samples
> > 7064            # samples_offset
> > 578             # bases
> > 0               # bases_left_clip
> > 0               # bases_right_clip
> > 128             # bases_offset
> > 0               # comments_size
> > 0               # comments_offset
> > 3.00            # version
> > 2               # sample_size
> > 2               # code_set
> > 171618          # private_size
> > 167072          # private_offset
> ...
>
> That looks _much_ better! The inclusion of bases and traces make it a "real"
> scf trace in my opinion. There's still lots of private data, but that's OK -
> that's what that block was designed for anyway.
>
> > The significant difference seems to be the version (2.10 -> 3.00)
> > and of course the "[bases]" block.
> > Did I misunderstand the SCF definition in the Staden Manual ??
> > It's possible to read those files with progs like 'chromas'.
>
> Assuming that the base and trace information is correct then I can see no
> reason why chromas (for example) wouldn't be able to read the files.
>
> > Well, but that doesn't answer the original question, if there's
> > a Mac Software which is able to read SCF file ...
> > Sorry Perry, there's lots of software for win or Unix systems,
> > I just don't know any other Mac software than SeqA3.x or EditView.
>
> There's quite a few Java trace viewers, so I'd expect those to work (as well
> as any Java app does).
>
> We did manage to (just about) get our Trev viewer working on the Mac, but it
> was a bit unstable and hideously slow compared to the Unix and PC version. (I
> don't know why, but I'm guessing at some of the Tk X emulation we used).
>
> James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
> Medical Research Council - Laboratory of Molecular Biology,
> Hills Road, Cambridge, CB2 2QH, England.
> Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/
>
> ---


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