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ACEDB data update 4-14 for C. elegans
The additions since 4-13 are:
- more genomic sequence data (there are now 986 cosmids totalling
- electronic entries in WBG 14 Number 2 have been added
- a physical map update (January 24)
- some medline references have been added together with connections
to sequences from these and cgc_references
- years have been added to wbg citations
- new data submitted by email to the CGC in Cambridge or direct to
Sylvia has been entered
- a number of errors and problems have been fixed
- names of proteins and motifs have been made more systematic, removing
The total database size after adding updates 4-1 to 4-14 is
approximately 260 Mbytes. The last 10% of the update, where the
protein naming is fixed, is unfortunately extremely slow to read in.
Also at this point the update window will flicker.
Instructions for obtaining updates/the whole thing
All the files are available in the following public access accounts
(anonymous ftp sites) accessible over internet:
ncbi.nlm.nih.gov (220.127.116.11) in the USA, in repository/acedb
ftp.sanger.ac.uk in England, in pub/acedb
lirmm.lirmm.fr (18.104.22.168) in France, in directory genome/acedb
In each case, log in as user "anonymous" and give a user identifier
as password. Remember to transfer the files in BINARY mode by
typing the word "binary" at the start of your ftp session. Many
thanks to NCBI for letting us share in their excellent resource.
password: your user id or email address
cd repository/acedb # change to relevant directoy
binary # IMPORTANT
dir # display files in this directory
cd ace4 # change to ace4 directory
get bin.sunos.4_1.tar.Z # get program
cd ../celegans # change to worm data directory
mget update* # get all update files
Get any update.4-n.tar.Z that you do not have already and read the
file NOTES before proceeding further.
Always get a copy of the INSTALL script. Move it and the .tar.Z files
into the home directory in which you are installing ACEDB. Type
"source INSTALL". Start acedb (normally by typing "acedb"), click
"Yes" to accept initialising the database if starting from scratch,
then choose "Add Update File" from the menu (right button), and press
"All updates" with the left mouse button.
If you have a problem making the program work, look at the section
on problems in NOTES, and if that fails to help, let us know.
Comments about the data should be sent to the data curator, Sylvia
Martinelli (sylvia at sanger.ac.uk).
Comments about the program, or the installation procedure, should be
sent to one of us:
Richard Durbin (rd at sanger.ac.uk)
Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)
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