Vector Cloning Software
jjowett at molbiol.ox.ac.uk
jjowett at molbiol.ox.ac.uk
Mon Dec 27 16:04:18 EST 1993
To Whom it may concern
For a while now I have been aghast at how difficult it has been to get a hold
of and find out about good programs for the PC that carry out cloning type
operations and keep track of DNA sequences- so that when you want to look
up a restriction map of a vector that maybe in it's 4th generation, you have
to sift through a pile of notes about which fragment came from where!
I am posting this message for those of you who have been similarly frustrated
to let you know about what a friend let me know of, and that is Vector PC. It
is the answer to the above problems!
We have been using Vector PC in our laboratory for several months
and have been very happy with its capabilities and performance.
The user interface is menu driven and easy to learn. The developers of
this program have made a significant effort to use terms that are
familiar to genetic engineers such that without prior experience of the
program, you can manipulate molecules and generate clones quickly
and easily. The beginners tutorial provides a good informative
introduction to the programs capabilities.
The program comes equipped with a wide variety of commonly
used cloning and expression plasmids in its own database which can be
searched using a wide a range of criteria from preferred host to
selection markers. You can add to the database any sequence that you
may acquire as well as having the program "read" them and install them
automatically from the Genbank database.
Perhaps the most useful feature of this program is the ability to
construct molecules from parent fragments as if you were cloning them
in the laboratory. This makes keeping track of which plasmid is
derived from which parent plasmid extremely straightforward, as the
program automatically remembers features of the parental fragments
such as genes, undefined open reading frames, markers and origins of
replication. Additionally the aforementioned features and more can be
added, deleted and edited at will using the vector editor - and all
descendants from that progenitor recalculated from the original source
fragment, making the introduction of new information into the database
straightforward and comprehensive. The construction of molecules can
also be made to include dummy fragments that have yet to be
sequenced and as with all fragments can have known restriction
endonuclease sites appended (such as might be determined by
endonuclease digestion and gel electrophoresis). The program includes
a restriction endonuclease database (also editable), that can be used to
do endonuclease site searches of any molecule when planning further
sub cloning steps. We have found this feature to be particularly helpful
abrogating the need to sift through numerous old sequences and
restriction site maps. The program also has useful graphical output to
generate hard copies for laboratory records.
Please email me if you require any more Info, I think the cost was about 1200
US Dollars, and it is written and sold by a company called Informax based in
the USA in Washington DC. In fact I heard that a windows version of this
software was in the pipeline, when I last called teh company.
It seems that software for science is seriously lacking, maybe we should quit
and learn how to program computers! it would appear there is a vacuum where
there could be many extremely useful programs - and I can't beleive they would
be beyond technical faesibility to write.
The above posting is solely my humble opinion!
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