ACEDB data release for C.elegans
rd at mrc-lmb.cam.ac.uk
Mon Jul 15 22:03:14 EST 1996
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ACEDB data updates WG1.4-4 and WS1.4-9 to 4-12 for C. elegans
You should be using these in conjunction with release 4_3 of the acedb
Reminder: there are now two versions of the C.elegans database. The
WS1 update series contains everything, whereas WG1 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.
The additions since WG1.4-3 and WS1.4-8 are:
for both types of update
- a physical map update with many changes (June 24th)
- some cgc references have been added (April 11th) also
a new set of connections between references and Loci
- cgc strains update (May)
- wbg subscribers update (May)
- wbg14.3 citations and abstracts
- genetic data left over from submissions for the new Worm map last year
(although a few outstanding points need clearing up next time)
- a set of transgenic strains from David Baillie has been added
- more expression data from Ian Hope and Donna Albertson and more pictures
and for just the complete database including sequences WS1.4-9
Data fom St Louis and Sanger Sequence databases taken in mid-June:
- There are now 1464 cosmids totalling 44,150,616 bases. We are
nearly half way!
- We are switching from using the PIR protein database for homology
searches to the TREMBL database, hence many PIR homologies are
being deleted and TR ones added.
The total database sizes after adding these updates are 370Mb for the
WS1 database (we said it would grow!) and around 65Mb for the WG1
It will take a long time to read in the WS1 updates, particularly
4-12. All four updates took us several hours.
For some reason, some of the Sequence-* map displays, which show the
status of the cosmids being sequenced, are not automatically updated
properly. If no coloured boxes are displayed when you show a Sequence
map, then please select "Recalculate" from the main menu. To avoid
you from having to do this every time, you should get write access
first, then save after recalculating.
Sorry, we inadvertently left out Restriction enzymes last time when we
were re-building the whole database. This meant that enzyme sites
could not be specified by name when using the DNA analysis tool.
Poetic justice caught up with Sylvia when teaching ACeDB to a class.
They have been added in this release.
We failed in the initial WG1 and WS1 releases to include the wscripts
directory containing the display_script for viewing the expression
pictures. They are included this time.
The DNA became inaccessible in the Macintosh version of WS1. We are
trying to resolve this problem before the next mac release.
The abstracts for the regional worm meetings 1996 did not make this
release, but will be in the next one. Plus further transposon mapping
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 (126.96.36.199) in the USA, in repository/acedb
ftp.sanger.ac.uk (188.8.131.52) in England, in pub/acedb
lirmm.lirmm.fr (184.108.40.206) 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_3.tar.Z # get program
cd ../celegans # change to worm data directory
mget update.WS1.* # get all WS1 update files
Get any update files 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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