Contig Analysis software

David Micklem drm21 at mole.bio.cam.ac.uk
Wed Jun 19 07:45:35 EST 1996


>Don Wigington (donw at ux5.lbl.gov) wrote:
>: Does any one know of good shareware for DNA clone contig analysis for a Mac?
>

We use AssemblyLign, from Kodak. It works very well and interfaces very
well with our DNA package, MacVector.  [Come to think of it, I think they
both just got bought by Oxford Molecular]

I particularly like one feature of AssemblyLign - it is possible to view
and edit your aligned sequences in a window where the bases are
represented by different coloured bars.  This makes it MUCH easier to spot
matches/mismatches, and allows a large stretch of sequence to be viewed at
a time.

It isn't without its problems though!  The (rather old) version we have is
very prone to crashing, and this makes some features totally unusable. 
Hopefully this has been fixed in more recent versions. 

As with MacVector, there are also several things they could have done to
make it much better.  The last time MacVector released a new version I
asked if they'd dealt with any of them, but they'd just added a bunch more
not-especially useful features instead.

(MacVector, if you're listening, I'd be happy to provide a list of
improvements that should be fairly trivial to implement - like being able
to paste sequence data into dialogue boxes!)

I saw a demo of a program (Sequencher IIRC) that seemed to be excellent
for analysing data from automated sequencers - it could read the
chromatograms, and display them, aligned the same way as the sequences. 
This should make it very easy to check discrepancies against the original
data.  I don't remember whether it could do the coloured-bar trick though!

No connection with any of the companies involved...

David

_____________________________________________________________
D.R.Micklem,
Wellcome/CRC Institute,       Time flies like an arrow...
Tennis Court Road,              
Cambridge CB2 1QR             Fruit flies like a banana.
UK                             
Tel: [+44] (0)1223 334129     Email:drm21 at mole.bio.cam.ac.uk
Fax: [+44] (0)1223 334089               
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