RESTRICTION MAPPING SOFTWARE

Harry Mangalam mangalam at uci.edu
Tue Apr 11 13:29:23 EST 1995


In article <3mcfiq$75h at ccshst05.cs.uoguelph.ca>, hsidhu at uoguelph.ca
(Harmandeep Sidhu) wrote:

> I have been trying to find some kind of software that can make linear or 
> circular maps from individual cosmid maps. I am using the partial 
> digestion method ( single enzyme ) to map the cosmid. Please help 
> me or my Boss will chain me to the wall and feed me bread and water for 
> the rest of the year.
> Thanking you in anticipation,
> Reg .


The usual questions... What platform?  Win/DOS/Unix/Mac?  What cost? 
Freeware. shareware, $$$ware?  For free on Macs, Gene Codes allows the
restriction mapper of their excellent fragment assembly program Sequencher
to operate ...unrestricted B).  Don Gilbert's Seqapp is a briliant, if
incomplete and somewhat buggy sequence analysis program (although you
wouldn't want to feed 20-30KB of sequence into it) and he has a new
program called Seqpup that operates on Macs, Windows and X that supposedly
does similar things.  I can also suggest Christian Marck's elegant DNA
Strider 1.2 for $200 (also Mac) if your cosmid seq are less than 32 KB and
for those with richer tastes, the DNASTAR Lasergene product (Mac, Windows)
is very good, especially if you want to allow a number of people access. 
Hitachi has updated and spiffed some of their previously execrable DNAsis
(Mac and PC) and IG's Geneworks is a nice product as well if $ are no
concern.
   There are some newish (if not gnuish) Windows products (almost all
$$ware).  Generunner is pretty good, but doesn't yet have the depth of the
Mac products and VectorNT is also a recent newcomer.

   Unix tools abound.  The easiest to set up is probably DNAworkbench
which is a large perl-based analysis script.  If on Suns or Linux, you
might look at Smith's GDE, which does restriction analysis.
   Being at Guelph, I would imagine that someone there has GCG running
which does eveything you want.

Cheers
harry
-- 
Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine,
      Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
                 --- knowledge is fractal ---
            http://hornet.mmg.uci.edu/~hjm/hjm.html
  Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW 




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