WormBase release WS112 now online
"WormBase" <[email protected]> Mon, 27 Oct 2003 12:16:40 -0500
| 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
roughly every 2 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.sanger.ac.uk/pub/wormbase/current_release/
New release of WormBase WS112, Wormpep112 and Wormrna112 Fri Oct 17 18:38:57 BST 2003
WS112 was built by Paul Davis
======================================================================
This directory includes:
i) database.WS112.*.tar.gz - compressed data for new release
ii) models.wrm.WS112 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS112-WS111.dbcomp - log file reporting difference from last release
v) wormpep112.tar.gz - full Wormpep distribution corresponding to WS112
vi) wormrna112.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS112.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) yk2orf.WS112.gz - Latest set of ORF connections to each Yuji Kohara EST clone
ix) gene_interpolated_map_positions.WS112.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS112.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS112.gz - for each C. elegans WormPep protein, lists Best blastp match to
human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins.
xii) best_blastp_hits_brigprot.WS112.gz - for each C. briggsae protein, lists Best blastp match to
human, fly, yeast, C. elegans, and SwissProt & Trembl proteins.
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS112
------------------------------------
brigdb : 2003-10-04 - updated
camace : 2003-10-06 - updated
citace : 2003-10-05 - updated
cshace : 2003-10-03 - updated
genace : 2003-10-08 - updated
stlace : 2003-10-03 - updated
Genome sequence composition:
----------------------------
WS112 WS111 change
----------------------------------------------
a 32367165 32367165 +0
c 17780236 17780236 +0
g 17757587 17757587 +0
t 32368413 32368413 +0
n 95 95 +0
- 0 0 +0
Total 100273496 100273496 +0
Wormpep data set:
----------------------------
There are 19935 CDS in autoace, 22215 when counting 2280 alternate splice forms.
The 22215 sequences contain 9,693,926 base pairs in total.
Modified entries 76
Deleted entries 23
New entries 45
Reappeared entries 0
Net change +22
Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed 4628 (20.8%)
Partially_confirmed 12102 (54.5%)
Predicted 5485 (24.7%)
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2415 (10.9%)
TrEMBL accessions 18223 (82.0%)
TrEMBLnew accessions 1559 (7.0%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22197 (99.9%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 4476
GeneModel correction progress WS111 -> WS112
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 681 | -104 |
St Louis | 432 | -32 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 0 | -30 |
St Louis | 32 | 0 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
i)Major overhaul of the tRNA predictions using latest tRNASCAN-SE-1.23 incorporated into WS112.
ii)Introduction of a large number of Micro array results connections to predicted genes and locus objects.
iii)Mitochondrial genome now has a laboratory id. designation for consistency.
iv)There has been an update to the functional annotations.
New Fixes:
----------
A fix has been done to brigpep to remove redundant/duplicated data.
Known Problems:
--------------
Seems to be a problem with stats for repeats matching exons for the Sanger 1/2(Sanger will investigate).
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
We will store GenBank GI numbers and cross reference them to our sequence objects so that you can navigate
between EMBL protein IDs and GenBank GI numbers.
Planned changes to WormBase front page. We are currently discussing whether to add more items to the WormBase
front page to better highlight new/interesting data in each new database release. E.g. 'click to see
list of new CGC worm-related papers included in database since last build'. If you have ideas for what you
would (or wouldn't!) like to see on our front page we would be interested in your opinions, please email us at
[email protected]
-===================================================================================-
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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