Sequence entry from digital image

core seq group neubauer at bms.com
Thu Oct 20 15:00:40 EST 1994


In article lld at taurus.fccc.edu, brunk at cygnus.fccc.edu (Brian Brunk) writes:
> Hi everyone,
> 	We have converted to powermacs in our new location.  We bought a 
> Princeton, NJ and would like to enter DNA sequence 
> from the digital image files.  Mol. Dyn. does not have powermac compatible 
> software to do this!  Do any of you know of software to facilitate sequence
> entry of from digital images that runs on the powermac.  It does not need
> to have automatic base calling, we can point to the correct base as one would
> do with a digitizer.  Any source (commercial or net) would be appreciated!
> 	Thanks!
> -Brian
> 
> Brian Brunk
> e-mail  brunkb at a1.mscf.upenn.edu
> phone  215-898-0243

Brian:
   We use the Bioimage film reader and Sequence Assembly Manager to read our films.
Works well with molecular dynamics phosphorimager tiff files (will import these files).
Software is expensive ($10-15K range) and runs on a sparcstation.  If you can find an
available Sparc 2 on your network, you can run the package and display it to your mac power PC running MacX.  The best thing about this software is not really the film reader ( which is acceptable if you have good gels ), but after you have edited or 
entered your sequence onto the image the image region used to call your base is available as a kind of hyperlink from the sequence assembly manager.  If you have a question about a base call, or there is an ambiguity in the consensus, all you do is 'click' on the base with your mouse and in a few seconds a window appears showing the region around the band used to call that base.  It makes assembly editing very easy.
Since the software can be displayed anywhere on your network, you might be able to
distribute the cost with other groups.

good luck

Mike Neubauer
neubauer at bms.com





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