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plasmidmap

Chris Barry chbarry at mackiller.llnl.gov
Tue Apr 16 15:01:24 EST 1996


Chris Barry wrote:
> 
> I have already looked in the manual to perform this operation and I
> don't see a refrence that shows me how to do it.
> 
> Does anyone know how gcg inserted a plock WITHIN the plasmid map that
> indicates the location on the insert. I have looked through the options
> in the WPI menu and there doesn't seem to be obvious switch. Thanks in
> advance.
> 
> Chris

I have recieved a lot of comments on this post. Most of which were
copies of what I read in the manual (not helpfull). Since it seem that
there are many users that don't know how to perform this function, I
thought a few of you might find this e-mail from gcg helpfull.

----------------------------Forwarded message-----------------------

Hello Chris,

>In your "EXAMPLE" of plasmidmap, there is a plasmid with a shaded block 
>designated as the insert (Fig 1, p14-4 program manual). How do you define 
>the region of the insert in the vector and how do you change the text in 
>the block? Thanks in advance.

PlasmidMap simply takes information in a specially formatted text file
and uses it to create the plasmidmap.

A good way to create a file which you can then edit to customize for
input into PlasmidMap is to run the GCG program 
o output results as a tick-style label file for PLASMIDMAP
o output results as a block-style label file for PLASMIDMAP

you can then edit the resulting file in any text editor (sorry, you
cannot 
edit this file inside of WPI) in order to add or modify the desired
blocks, ticks and ranges.

We must be looking at different versions of the program manual,
because in the current manual there is no figure on page 14-4.
I will assume that figure 1 in the current document is the same as
the one you are referring to.

>PS It would be helpfull if the examples contained ALL the parameters used 
>to generat the image

The input file used to create this figure is included in the
documentation
for PlasmidMap in the section labelled "Input FIles" after the
subheading 
"STYLE".

In addition, all examples can be generated, and all input files used to 
create the  examples are available on-line if you know how to access
them.

In the example that generated Figure 1, the input file used for
plasmidmap was
pgamma.fil  (this was typed in to the program as @pgamma.fil to indicate
that
this file actually contained a list of input files to be used to
generate the 
plasmidmap)

At a GCG command-line prompt (not in WPI) you can view this file by
typing in the
command:

 typedata pgamma.fil

This will display it's contents as:

..
GenDocData:pgamma.tick
GenDocData:pgamma.ranges

The file GenDocData:pgamma.ranges is the input file which actually
contains the line which creates the shaded box labelled "Insert".  The
actual file 
can be viewed with the command:

 typedata GenDocData:pgamma.ranges

Here is the entire contents of this file:
----------------------
Ranges for pGamma.Seq:

assembled From EMBL:Pbr322

locus       pbr322       4363 bp    dna   circular  updated   02/22/85
definition  plasmid pbr322, complete genome.

and from GenDocData:gamma.seq

Name     From       To   Strand    Color  Symbol1  Symbol2    Style ..

! the genes from pbr322

Tet_Resistance   86       1276        +    Black       <       <
Range
Beta_Lactamase 4086       3298        -    Black       <       <
Range

! human fetal beta globin a gamma coding regions

CAP_Site 4566   4566    .    Black   .     .     Tick
_        4618   4709    .    Black   |     |    Range
A_Gamma  4832   5054    .    Black   |     |    Range

! blocks for vector and insert

pBR322_cut_at_RI    1   4363    +    Blue    ]     ]     Range
Insert           4364   5246    +    Blue    |     |     Block
------------------------------

The line which creates the shaded box labelled "Insert" is the last
line,
which reads:

Insert           4364   5246    +    Blue    |     |     Block

If you instead wanted to label this "My Insert", you could change the
line
to read:

My_Insert        4364   5246    +    Blue    |     |     Block

More information on the format of the lines in this file can be found
under the 
heading "Input FIles" in the plasmidmap documentation.

I hope that you find this information helpful.

Regards,
Lynn Miller
--------------------------------------------------------------
Lynn Miller                   ||   phone: (608) 231-5200
Technical Support Coordinator ||     fax: (608) 231-5202
Genetics Computer Group, Inc. ||  e-mail: help at gcg.com
575 Science Drive             ||  e-mail: Lynn.Miller at gcg.com
Madison, WI  53711-1060 USA   ||  e-mail: miller at gcg.com
                              ||     WWW: http://www.gcg.com
--------------------------------------------------------------



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