IUBio

Can you help?

Shiping Zhang ping at bnlux1.bnl.gov
Thu Jul 27 20:12:15 EST 1995


In article <myersm-2707951252040001 at shioh_pc.rockefeller.edu>,
Michael Myers <myersm at rockvax.rockefeller.edu> wrote:
>In article <3v386h$cnk at dartvax.dartmouth.edu>, Bob.Gross at dartmouth.edu
>(Robert H. Gross) wrote:
>
>>Damian -
>>
>>There is a program called the Gene Construction Kit which seems like it
>>will meet your needs. A demo is availabe by FTP from most Info-Mac
>>sites and from Don Gilbert's site at Indiana. You can also contact the
>>company (Textco) directly at textco at valley.net.
>>
>
>I apologize that the following is so long. I got a bit carried away!
>Continue only if you're interested in my personal opinions regarding GCK,
>MacPlasmap, and GCG.
>
>I have used Gene Construction Kit a fair amount. First, you should know
>it's fairly expensive. I believe nearly $1000, make sure you ask about an
>academic discount. Secondly, while some of its features are quite nice, it
>has some annoying qualities. For example
> [...]

Execept lacking the feature of drawing a graphic map (will be added in the
future), a program at the WWW site (under the DNA sequence analysis group)

http://genome1.bio.bnl.gov/bbq.html

can do quite a lot of restriction enzyme analysis of DNA sequences.  It can
also give information about restriction enzymes such as commercial availability methylation, references, all from REBASE.  Here are some example output.

-ping


Example1:

		Plasmid ColE1, compl (6646 bps)

      Enzymes  Sequences   Sites  Fragments in order
      of cuts   of cuts   of cuts  of cuts  of size

  1.    AvaII     ggacc      114      207     2239
  2.    AvaII     ggacc      535      421     1689
  3.    AvaII     ggtcc     2224     1689     1188
  4.    AvaII     ggacc     4463     2239      686
  5.    SacII    ccgcgg     5149      686      421
  6.     PstI    ctgcag     5284      135      207
  7.     PstI    ctgcag     5365       81      135
  8.     PstI    ctgcag     6553     1188       81

	Following enzymes cut only once:
               SacII     

Example2:

		ColE1 (6646 bps) digested with PstI, AvaII and SacII

size scale        2560      1280       640       320       160        80
                    .         .         .         .         .         .         

           ColE1      |   |    |       |      |         |     |       |         

	Following enzymes cut only once:
               SacII     

(This gives an estimated gel pattern of the fragments of digestion based
on the assumption that the migration rate of a fragment is reciprocally
proportional to log2(size). Anyone has a better theory?)

Example3:

             CE1CG13: 6646 bps. Each dash is about 110 bps
        AagI       --------------------1---------------------------------------
        AaqI       --------1---------------------------------------------------
      * AatI       -----------------------1-------------------1----------------
        AcaI       -1------------------------------------------------------1---
        AcaIV      ---1--1---11---2--12---11--------11--------1---------1------
        Acc38I     ---------2-11----1-1--1------1------1---11------------------
        AccB1I     ------------------1------------------1----------------------
      * AccI       -------------1------1--------------------------1------------
        [...]

(This shows digestion maps of all enzymes in the REBASE database.  Enzymes
marked with asterisks are commercially available (at the time the database
is compiled).  The numbers indicate the number of cuts in the region of
a dash length. Enzymes that don't cut or cut only once are listed at the end
(omitted here).)




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