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ACEDB data release WS5 for C.elegans

Richard Durbin rd at sanger.ac.uk
Fri Dec 18 10:35:00 EST 1998

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New ACEDB data release WS6 for C. elegans

This data release contains the genome sequence as reported last week
in Science: "Genome Sequence of the Nematode Caenorhabditis elegans. A
Platform for Investigating Biology", The C. elegans Sequencing
Consortium, Science 282:2012-2018 (1998).  The genomic DNA is linked
up in 6 chromosomes, so you can potentially scroll from one end to the
other of a chromosome in the sequence display window - some unfinished
data is linked in, but there are regions with blocks of N's where gaps
are still being filled.  Other data types have also been updated.

Like the last release (WS5), this release is made as a set of
compressed database files (database.WS6.4-0.tar.Z,
database.WS6.4-1.tar.Z etc. up to 4-6), which the INSTALL script will
unpack into a working database - there is no need to "Add updates"
from inside acedb as previously.

You will need nearly 2 GB of disk space to install.  Once installation
is finished you can remove the database.*.tar.Z files, leaving around
1.4 GB for the database plus program etc..

You MUST have a copy of the INSTALL script from September 1998 or

If you have a working acedb version built with the WS4 or a previous
series, 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.WS3...tar.Z or
rawdata/update.WS3... files.

You should be using these updates in conjunction with release 4_5 of
the acedb software (released in August 1997).  If you have a working
acedb version from since then, you do not need a new copy of the
program (the bin.<operating system>.* file).  If you are installing
into a new directory you will need an appropriate binary from the
.../acedb/celegans/ace4/ directory.

There is no WG6 database, containing the genetic data without the
sequence data.

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 in the USA, in repository/acedb
  ftp.sanger.ac.uk in England, in pub/acedb
  lirmm.lirmm.fr in France, in directory genome/acedb

In each case, log in as user "anonymous" and give an email address
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.


ftp ncbi.nlm.nih.gov
login: anonymous
password: your user id or email address
cd repository/acedb             # change to relevant directoy
binary				# IMPORTANT
dir				# display files in this directory
get INSTALL			# always get this
cd ace4				# change to ace4 directory
get bin.solaris.4_5e.tar.Z	# get program
cd ../celegans			# change to worm data directory
mget database.WS6.*		# get all WS5 database files


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
"csh INSTALL".

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 installation procedure, should be sent to Richard
Durbin (rd at sanger.ac.uk)

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