Shareware cloning program that reads genbank feature tables?

Peter Rice rice at embl-heidelberg.de
Wed Jun 22 03:43:11 EST 1994


In article <2to924$pk8 at news.mic.ucla.edu>, Robert Lloyd
<rlloyd at inherit2.dna.ucla.edu> writes:
> 	The subject line says most of it.  What I would like to know is if a
> program is available that  will read a genbank style file and then do
> simple DNA manipulations (splicing two DNA fragments together, deleting
> sections, inverting a file etc.) while  maintaining the feature tables of
> a genbank file ?  Of course writing a text file of the feature table
> would help _a lot_.  Several commercial programs read these feature
> tables but none seem capable of manipulating and then exporting them.

There is a program in the EGCG package (extended GCG) that can do most of this.
It allows you to edit an EMBL or GenBank entry (the feature table syntax is the
same for both) and insert/delete/reverse. We have a request from an EMBL user
to include the feature table from another entry when inserting additional
sequence but have not yet implemented it.

The EGCG package is available by anonymous ftp from ftp.embl-heidelberg.de
in directory pub/software/vax/egcg. You must have the full GCG package in
order to use EGCG.

The program in question is NEWFEATURES. At present it is only available in
VMS versions of EGCG. A unix version is planned, but we have not yet looked
into the problems of converting the screen handling so it could be delayed.

 -----------------------------------------------------------------------------
 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice at EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       69012 Heidelberg
 Fax:     +49-6221-387306                     |       Germany



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