Genbank to GCG Help!

Gerard Stafleu gerard at uwovax.uwo.ca
Thu Mar 31 07:43:28 EST 1994

In article <0097C37B.32C6EB80 at vms.csd.mu.edu>, 6566friedman at vms.csd.mu.edu writes:
> I am looking for some technical assistance in converting the genbank 
> database available from the NLM archive into a VMS GCG usable format.  
> The LZ decompression file from ncbi.nlm.nih.gov bombed.  I understand 
> that LVDCMP.EXE from net.bio.net works better.  However our systems 
> analyst doesn't know what to do with the many files that output when we 
> run "Genbank to GCG".  Any suggestions???

Make them into a GCG library, as follows.  Put the files (.seq, .ref, .names  
etc) in a subdirectory.  All these files have the same part before the 
period, say COWS.  Say your username is friedman, you could put 
them in [FRIEDMAN.LIBS].  If you named the retrieved file GENBANK.COWS, 
you would now have the file [FRIEDMAN.LIBS]GENBANK.COWS.

Then define a logical name for the library, for example: 

$ assign [friedman.libs]cows cows

Now run genbanktogcg:

$ GenbankToGCG/dir=[friedman.libs]/ln=cows/out=cows [friedman.libs]genbank.cows

/dir=[friedman.libs] tells the program where to put the .seq etc. files, 
/ln=cows is the library name (the logical name, officially), /out=cows 
makes sure that the files are called cows.seq etc.

You can now access the sequences as you do from any other library, say

   names cows:*

will show you all the names in te cows library.  

If you want to add new files to the library, just append the new file 
you retrieved from genbank to the original, and run the whole thing 
through genbanktogcg again. (you don't need to redefine the logical 

Gerard Stafleu
email: gerard at uwo.ca
ITS, University of Western Ontario,
London, Ontario, Canada N6A 5B7

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