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).)
