** WARNING: This release is only complete at the NCBI site in the USA.
** We plan to bring the UK and France sites up to date within the next
** day or two.
This is a broadcast message to the ACEDB mailing list and related
newsgroups. If you are on the explicit mailing list and do not want
to be, please send email to rd at sanger.ac.uk.
New ACEDB data release WG3.4-2 and WS3.4-17 for C. elegans
With this release we are once again starting a new series of database
updates from scratch again, rather than adding on to WS2.4-20. The
new series is called WS3 (and correspondingly WG3 for the version
Because both series are new, you must get all the updates from the
series you want (WS3 or WG3), and rebuild a new database using them.
Fortunately, it will be much faster reading in the seventeen new WS3
updates than twenty-four of the WS2 series.
(N.B. at the end of this file is a list of the contents of each
If you have a working acedb version built with the WS2 series, you
must do two things:
(1) you must remove your current database/ directory (ideally after
backing it up in case of difficulties). As well as removing the
database directory, you can also remove any update.WS2...tar.Z or
(2) you must get a new copy of the INSTALL script, as well as all
the new WS3 updates.
If you do not remove the contents of the database directory, when
you start up acedb it will still say "WS2" in the title bar, and will
not be able to load the WS3 updates. When you have emptied it
properly, it will ask if you want to reinitialise, and put WS3 in
The software has not changed. You should be using these updates in
conjunction with release 4_3 of the acedb software.
Reminder: there are now two versions of the C.elegans database. The
WS3 update series contains everything, whereas the WG3 update series
contains all data except sequences and directly related material
(proteins, motifs etc.), for those with limited resources.
The additions since the last release are:
for both types of update
- a physical map update with a few changes (mid May)
- accumulated genetic data corrections
- from CGC : bibliography, wbg subscribers and strains (May)
- from Leon Avery : worm meeting absracts with connections to genes etc.
and for just the complete database including sequences (WS3.4-17)
Data fom St Louis and Sanger Sequence databases taken in mid-May:
- There are now 2237 (2177 before) cosmids totalling 66969575
(65222006 before) bases.
- EMBL50 Sequence, dna and full embl text descriptions
The total database sizes after adding these updates are around 560MB
for the WS3 database and around 60MB for the WG3 database.
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 (188.8.131.52) in the USA, in repository/acedb
ftp.sanger.ac.uk (184.108.40.206) in England, in pub/acedb
lirmm.lirmm.fr (220.127.116.11) 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.WS3.* # 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)
UPDATE FILE CONTENTS (BRIEFLY)
ws3.4-1 = geneace 1st half (i.e. non sequence material)
ws3.4-2 = geneace 2nd half (i.e. non sequence material)
ws3.4-3 = file1 (sequence_ace bits & pieces)
ws3.4-4 = peptide file
ws3.4-5 = dna1
ws3.4-6 = dna2
ws3.4-7 = dna3
ws3.4-8 = dna4
ws3.4-9 = dna5
ws3.4-10 = protein1
ws3.4-11 = protein2
ws3.4-12 = protein3
ws3.4-13 = sequence1
ws3.4-14 = sequence2
ws3.4-15 = sequence3
ws3.4-16 = sequence4
ws3.4-17 = sequence5 & motif & general fixes