C2G@VAX5.CIT.CORNELL.EDU (10/17/90)
Can anyone name a good software package for recombinant DNA analysis?
Here's all it need do:
o Know where restriction sites are.
o Refercence functional information about a location.
o Be able to ligate several fragments (defined as above) together.
o Produce cleavage, cutter info. on ligated sequences, use these
new ligated sequences as sequences from which new fragments can be taken.
Thats roughly it. I'm not talking GCG, Intelligenetics style sequence analysis,
just knwledge about cleavage and functional locations. That is,
will the program be satisfied if all I tell it is : "I have a 300 bp long
sequence. EcoRI cuts at positions 23, 67, and 112. BglII cuts at 24"
A blank line with 4 nothces in it. (Or cicle, if circular.)
I have a feeling there are some PC-based programs out there that do just
this, but that I'm not aware of. Anybody with even a vauge hint or reference,
(or if you're looking for the same thing) please let me know. I know
little about this area and would appreciate the help. (Note:
typo above. Have BglII cut at 34.)
Thank You,
Barry IsralewitzC2G@VAX5.CIT.CORNELL.EDU (10/17/90)
Can anybody name a good software package that
C2G@VAX5.CIT.CORNELL.EDU (10/17/90)
Can anyone name a good software package that can analyze DNA fragment
information on the level of functional sites and cleavage sites? The program only needs to:
o Know locations of cleavage sites.
o Know locations of functional sites (entered by user)
o Ligate fragments or sections as described above to make a new fragment
or plasmid.
o Provide some searching and display options.
For instance, I should be able to the cell software, " I have a plasmid,
350 bp long. EcoRI cuts at positions 23, 102, and 140. BglI cuts at C2G@VAX5.CIT.CORNELL.EDU (10/17/90)
Can anyone name a good software package that can analyze DNA fragment
information on the level of functional sites and cleavage sites?
The program would only need to:
o Know locations of cleavage sites on a fragment (entered by user or
derived from sequence information)
o Know location of functional sites (chosen by user)
o Ligate fragments or sections of fragments to make new fragments,
which can then be ligated themselves.
o Provide some searching and display options, and make
clear relation between origin and descendant sequences.
For instance, I should be able to tell the program, it knowing at first
nothing about my sequence, "This is a fragment 300 bp long, with
EcoRI restriction sites at 23, 123, and 240 and a BglII site at 180."
Thats roughly it. I don't need sequence analysis as in GCG type
programs, just simple ligation. I just told the program
about a blank line with 4 hatches, and thats all it need know to
keep track of restriction sites.
I have a feeling there are some PC based programs out there that do
just what I'm looking for, but that I'm not now aware of. Anyone
with even a vauge hint or reference, post here or contact me at
c2g@vax5.cit.cornell.edu.
Thank you,
Barry Isralewitzmn5y@krebs.acc.Virginia.EDU (Mukund Nori) (10/17/90)
There is one program that will do what I believe you need it for. It is
called DM5. I do not think it is shareware. We use it on our mainframe
UNIX systems, but it works on PCs too and it is small. The person to
contact here would be Dr. William Pearson. I could ask him for you and
post a response if positive.
Take care.
******************************************************************
___Raistlin___ Mukund Nori
Raistlin@Virginia.EDU mn5y@krebs.acc.Virginia.EDU
"VIOLENCE IS THE LAST RESORT OF THE INCOMPETENT" Asimov