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 at vax5.cit.cornell.edu.