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GeneRunner - Molbio Software for MS Windows

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Tue Apr 27 18:37:06 EST 1993

   Well, it had to come.  Molbio comes to Windows.  There was an intriguing
ad in the back of Science the other week (but with no phone #) and after a
bit of poking around, I found the phone number of the maker (Hastings
Software - 914 969 0855; 914 376 4433 (fax) and requested their demo.
   There will apparently be a longer, more exhaustive review on it in
"Biotechnology Software" (not by me) either this month or next, but here's
my initial take on it.

   It IS a Windows application!  A truly Gatesian Molbio program.  And
overall it's quite a respectable piece of work.  Think of DNA Strider "Pro"
for Windows and you have a good idea of what it does.  My machine is an old
25Mhz 386/387; 8MB, caching SCSI controller driving a 340 MB Maxtor, and a
sw-cached ESDI 150 MB Seagate.

It took about 15 s to load - not too bad for an old 386, but not quite as
snappy as Strider on a Quadra.
- It cuts DNA of ANY size (ie - no 32 kb size restriction) and quite
respectably fast - the demo has that stinking restriction that you can't
use your own sequence, but in cutting lambda DNA (~50kb) it buzzed thru it
in 21 sec with 212 enzymes.  I'm a fool for RE analysis and theirs is very
nice to use - you can select enzymes by about 30 criteria, including # of
cuts (< +/or >), length of recognition sequence (< +/or >), overhang
length, type of overhang, [salt], etc, and unlike some other programs, has
a nice default setting.
   The demo comes with one RE list and the real program comes with RE lists
from several companies. 

   The restriction mapping output is OK but not spectacular.  Specifically
it doesn't have a nice text output, with REs marked on top, with optional
translation below, like Strider or DNASTAR Mac (although you can get the
sequence with 6 frame translation separately).  It's graphical output is
the ladder format with each RE pattern as a rung, or as a simple cut map
with a few enzymes.

   The visual editor can display color/bw residues, 1/3 letter codes for
aas, single/double strands, upper/lower case, in 3/10 residue grouping,
with reverse highlighting for selection, just as you'd expect it to.  If
you have a sound card, it'll speak the sequences back to you.
   While it can read Genbank format, it doesn't read much else very well
and the authors were unaware of Don Gilbert's Readseq code that could do
that for them.  It can display GB features and annotations (in a little
viewer as the original text, not as diagrams, like Geneworks and

   It has a pretty large number of features for oligo and PCR analysis,
including designing sequencing oligos, reverse translation for degenerate
screening, etc.

   It also has a special section for electronic cloning (that I have not
yet investigated to a great extent) but according to the instruction sheets
that come with the demo, it allows e-clooning and generates a report on
each step of the procedure, something like Gene Construction Kit for the

   It does NOT have any kind of protein analysis tools at all, nor will it
do multiple alignments (but Macaw does that very nicely) nor does it have
any kind of fragment assembly capability, but the salescritter to whom I
spoke said that the frag assembly bit was their next project.  Due Real
Soon Now.
   It also has no builtin Internet capabilities like Don Gilbert's SeqApp.  

   Windows being Windows, I had all sorts of lockups and UAEs during my
trials with it, but I couldn't say how much of the problems were due to
GeneRunner and how much were due to Windows.  It seemed less stable than MS
Word and Macaw, but more stable than most of my netwoking software.

  Overall, relative to its capabilities, it is certainly worth looking at,
especially because of it's introductory pricing - $299 std, $249 acad until
Aug 1st, $995 afterwards.

   Hastings software has stated that they had no objection to distribution
of the demo, so tomorrow (forgot the disk at home), I'll zip the disk and
put it up for anon ftp.


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