WormBase release WS86 now online
"WormBase" <[email protected]> Sat, 7 Sep 2002 03:33:27 -0400
| Newsgroups | gmane.science.biology.wormbase.announce |
|---|---|
| Message-ID | <[email protected]> |
This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated. New releases occur
every two weeks.
The text of the AceDB release notes, which contains highlights of the
new data is attached. You can download the full AceDB files from:
ftp://ftp.wormbase.org/pub/wormbase/current_release/
New Release of acedb WS86, Wormpep86 and Wormrna86 Fri Sep 6 13:26:51 BST 2002
======================================================================
This directory includes:
i) database.WS86.*.tar.gz - compressed data for new release
ii) models.wrm.WS86 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS86-WS85.dbcomp - log file reporting difference from last release
v) wormpep86.tar.gz - full Wormpep distribution corresponding to WS86
vi) wormrna86.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS86.gz - DNA sequences of all genes confirmed by EST &/or cDNA
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS86
------------------------------------
brigdb : 2002-08-30 - updated
camace : 2002-09-02 - updated
citace : 2002-08-30 - updated
cshace : 2002-08-28 - updated
genace : 2002-09-02 - updated
stlace : 2002-08-30 - updated
Genome sequence composition:
----------------------------
WS86 WS85 change
----------------------------------------------
a 32352971 32344742 +8229
c 17772485 17767680 +4805
g 17750022 17745321 +4701
t 32354695 32346297 +8398
n 95 95 +0
- 2000 62800 -60800
Total 100232268 100266935 -34667
Wormpep data set:
----------------------------
There are 19486 CDS in autoace, 20878 when counting 1392 alternate splice forms.
The 20878 sequences contain 9,233,930 base pairs in total.
Modified entries 45
Deleted entries 18
New entries 52
Reappeared entries 0
Net change +34
GeneModel correction progress WS85 -> WS86
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 1566 | -50 |
St Louis | 412 | -51 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 26 | -3 |
St Louis | 181 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_II sequence AF016683
CHROMOSOME_II sequence AF016683
CHROMOSOME_II sequence U23175
CHROMOSOME_II sequence U23175
CHROMOSOME_IV sequence AC006701
CHROMOSOME_IV sequence AC025724
CHROMOSOME_IV sequence AC025724
CHROMOSOME_IV sequence AF125445
CHROMOSOME_IV sequence AF125445
CHROMOSOME_IV sequence AF038618
----------------------------------------------------------------
Remaining gaps:
---------------
For more info mail [email protected]
# Gap on Chromosome III is covered by a 950Kb SseI fragment
III 1005794 1028769 37 F AC087078.1 1 22976 +
III 1028770 1029769 38 N 1000
III 1029770 1055632 39 F AC092690.1 1 25863 +
# Gap on Chromosome X is covered by YAC clones in production at St Louis
X 1 2649 1 F AL031272.2 1 2649 +
X 2650 3649 2 N 1000
X 3650 14860 3 F AC087735.3 1 11211 +
New Data:
---------
New yeast and fly protein data sets were used in the WUBLAST analysis. Both datasets
now contain expanded information, concerning SGD and FLYBASE database accessions
and identifiers, and fly/yeast gene names where known.
Protein database identifiers are now searchable in the database, i.e. you can now
search for the Swissprot protein from the WormBase front page using either the
accession "Q17606" or the ID "RL24_CAEEL".
Two gaps were closed by St. Louis for chromosome X (see above for details of remaining
gaps). The new clones covering the gaps at the start of this chromosome are Y15D9A and
Y108F1.
As a result of a new script by Chao-Kung Chen, we now systematically extract gene
name information from EMBL and use this to update our database. In this release
nearly a 1000 gene names have updated/new information based on this new approach.
This approach allows us to make new connections between a locus name and the
corresponding sequence name. This work is ongoing and will see many non-CGC-approved
gene names added as 'Other names' to the correct CGC gene name, thus making it
easier to find your gene of interest.
New Fixes:
----------
Known Problems:
--------------
The new clones that filled the two gaps on chromosome X do not yet have any accession
numbers and therefore these are missing from the agp files. Should be fixed by
next release.
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
We propose to change our build schedule for the next release. WS87 will be finished
in three weeks time rather than two. This extra week will enable to undergo a fundamental
change in how we organise our database build procedure. The net result of this will be
that all BLAST homologies in the database will be current and up to date. We currently
have a slight discrepancy where the Wormpep database used for BLAST analysis corresponds
to the last build of the database. I.e. WS86 used protein info from Wormpep 85.
Quick installation guide for UNIX/Linux systems
-----------------------------------------------
1. Create a new directory to contain your copy of WormBase,
e.g. /users/yourname/wormbase
2. Unpack and untar all of the database.*.tar.gz files into
this directory. You will need approximately 2-3 Gb of disk space.
3. Obtain and install a suitable acedb binary for your system
(available from www.acedb.org).
4. Use the acedb 'xace' program to open your database, e.g.
type 'xace /users/yourname/wormbase' at the command prompt.
5. See the acedb website for more information about acedb and
using xace.
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