WormBase release WS88 now online
"WormBase" <[email protected]> Sat, 12 Oct 2002 03:10:21 -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 WS88, Wormpep88 and Wormrna88 11/10/02
============================================================
This directory includes:
i) database.WS88.*.tar.gz - compressed data for new release
ii) models.wrm.WS88 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS88-WS87.dbcomp - log file reporting difference from last release
v) wormpep88.tar.gz - full Wormpep distribution corresponding to WS88
vi) wormrna88.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS88.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 WS88
------------------------------------
brigdb : 2002-09-29 - updated
camace : 2002-09-30 - updated
citace : 2002-09-29 - updated
cshace : 2002-08-28
genace : 2002-09-30 - updated
stlace : 2002-09-29 - updated
Genome sequence composition:
----------------------------
WS88 WS87 change
----------------------------------------------
A 32352971 32352971 +0
C 17772485 17772485 +0
G 17750022 17750022 +0
T 32354695 32354695 +0
N 95 95 +0
- 2000 2000 +0
Total 100232268 100232268 +0
Wormpep data set:
-----------------
There are 19,501 CDS in autoace, 20,931 when counting 1,430 alternate splice forms.
The 20,931 sequences contain 9,259,541 base pairs in total.
Modified entries 118
Deleted entries 33
New entries 83
Reappeared entries 0
Net change +50
Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed 3411 (16.3%)
Partially_confirmed 9124 (43.6%)
Predicted 8396 (40.1%)
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2088 (10.0%)
TrEMBL accessions 17242 (82.4%)
TrEMBLnew accessions 1307 (6.2%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 20772 (99.2%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 3322
GeneModel correction progress WS87 -> WS88
-----------------------------------------
+---------+--------+
Confirmed introns not is a CDS gene model: | Introns | Change |
+---------+--------+
Cambridge | 1298 | -247 |
St Louis | 358 | -53 |
+---------+--------+
+---------+--------+
Known repeat families that overlap predicted exons: | Introns | Change |
+---------+--------+
Cambridge | 28 | 2 |
St Louis | 180 | -1 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
CHROMOSOME_III sequence AF040644
CHROMOSOME_IV sequence AF036703
CHROMOSOME_IV sequence U40798
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:
---------
C.briggsae non-coding RNA genes added to the cb25.agp assembly data.
New Fixes:
----------
Updated the Parasitic nematode EST sequences.
Removed empty sequence objects made by cross-reference to (mis)named
OST DNA sequences.
Increased connections between mRNAs and CDS to 75%.
Naming of Gadfly proteins in the database has been corrected.
Known Problems:
--------------
Bad sequence objects left over from removal of emblace (see below).
Other Changes:
--------------
*IMPORTANT* - The data previously contained in emblace has been retired.
Much of this was redundant (e.g. the EMBL:<id> objects existed as <acc>
objects used in BLAT mapping mRNAs to the genome sequence). emblace
derived objects have the timestamp 'emblace' and are usually named
EMBL:*. Connections to emblace objects have been removed from camace and
geneace. There remain 475 EMBL:* objects in WS88 derived from citace via
cross-reference to Paper and Expr_patterns objects.
*KEYSETS* - Lincoln had asked for a list of CDS sequences which are
supported by mRNA/EST/OST data. Due to the limit on subclasses from a
class in acedb databases we cannot produce this at the moment. A working
solution is to generate and save in the database release keysets of objects
as required. This is a scaleable method for providing quick access to a set
of often asked for queries. See <web> pages for more information.
Proposed Changes / Forthcoming Data:
------------------------------------
Further tidying of data sets to remove deprecated sequence objects.
Re-working of the Matching_cDNA tags linking mRNA/EST to CDS.
Pilot project to map sequence features to the genome sequence.
-================================================================================-
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.
____________ END _____________