I discovered that the programs using restriction enzymes do not work
on my installations of EMBOSS:
ERROR application terminated
EMBOSS An error in remap.c at line 236:
Cannot locate enzyme file. Run REBASEEXTRACT
So I tried to follow the instructions on the EMBOSS site at sourceforge:
------------------------------------------------------------------------
--------
Rebase is the restriction enzyme database maintained by New England
Biolabs. It is needed for programs such as remap and restrict.
The latest version of Rebase can be obtained by anonymous FTP.3.10
EMBOSS needs the
withrefm
file. The data is extracted for EMBOSS with the program rebaseextract.
% mkdir /site/prog/emboss/data/REBASE
% rebaseextract
Extract data from REBASE
Full pathname of WITHREFM: /data/rebase/withrefm.208
Rebase is now installed and ready to use.
------------------------------------------------------
... FTP.3.10
ftp://ftp.ebi.ac.uk/pub/databases/rebase
------------------------------------------------------
1. I downloaded the file withrefm.912.Z and extracted the file
withrefm.912
2. I attempted to make a directory called REBASE but it already
existed at /usr/local/EMBOSS-3.0.0/emboss/data/REBASE on my OS X
installation. The contents were;
Makefile.am Makefile.in dummyfile
3. OK, so I tried to run rebaseextract:
david: rebaseextract
Extract data from REBASE
Full pathname of WITHREFM file: /Users/david/withrefm.912
Full pathname of PROTO file:
Nothing in the instructions about a PROTO file. Go back to the ftp
site and download proto.912
Full pathname of PROTO file: /Users/david/proto.912
EMBOSS An error in ajfile.c at line 2173:
Cannot write to file /usr/local/share/EMBOSS/data/REBASE/embossre.enz
4. So I check whether there is a directory /usr/local/share/EMBOSS/
data/REBASE. There is, with a file entitled "dummyfile".
5. Give up. Life's too short to learn C.
David
___________________________________________________
Dr. David P. Leader, Faculty of Biomedical & Life Sciences,
University of Glasgow, Glasgow G12 8QQ, UK
Phone: +44 (0)141 330 5905
http://doolittle.ibls.gla.ac.uk/leader
http://motif.gla.ac.uk/
The University of Glasgow, charity number SC004401
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