WormBase release WS109 now online
"WormBase" <[email protected]> Sun, 14 Sep 2003 00:57:10 -0400
| Newsgroups | gmane.science.biology.wormbase.announce,gmane.science.biology.wormbase.general |
|---|---|
| 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 WS109, Wormpep109 and Wormrna109 Fri Sep 5 15:29:03 BST 2003
WS109 was built by Anthony Rogers
======================================================================
This directory includes:
i) database.WS109.*.tar.gz - compressed data for new release
ii) models.wrm.WS109 - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
iv) WS109-WS108.dbcomp - log file reporting difference from last release
v) wormpep109.tar.gz - full Wormpep distribution corresponding to WS109
vi) wormrna109.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
vii) confirmed_genes.WS109.gz - DNA sequences of all genes confirmed by EST &/or cDNA
viii) yk2orf.WS109.gz - Latest set of ORF connections to each Yuji Kohara EST clone
ix) gene_interpolated_map_positions.WS109.gz - Interpolated map positions for each coding/RNA gene
x) clone_interpolated_map_positions.WS109.gz - Interpolated map positions for each clone
xi) best_blastp_hits.WS109.gz - for each C. elegans WormPep protein, lists Best blastp match to
human, fly, yeast, C. briggsae, and SwissProt & Trembl proteins.
Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE
Primary databases used in build WS109
------------------------------------
brigdb : 2003-08-22 - updated
camace : 2003-08-26 - updated
citace : 2003-08-25 - updated
cshace : 2003-07-22
genace : 2003-08-29 - updated
stlace : 2003-08-22 - updated
Genome sequence composition:
----------------------------
WS109 WS108 change
----------------------------------------------
a 32367165 32367166 -1
c 17780236 17780238 -2
g 17757587 17757588 -1
t 32368413 32368415 -2
n 95 95 +0
- 0 0 +0
Total 100273496 100273502 -6
6bp (GATCTC) was removed from the 5' end of K12B6 (and the corresponding
region of the overlapping clone (F31F7)). A finisher had chosen the wrong GATC site.
This 6 bp sequence was then duplicated when F31F7 was finished, and the overlap with K12B6 was
added.
Wormpep data set:
----------------------------
There are 19928 CDS in autoace, 22128 when counting 2200 alternate splice forms.
The 22128 sequences contain base pairs in total.
Modified entries 143
Deleted entries 28
New entries 42
Reappeared entries 14
Status of entries: Confidence level of prediction
-------------------------------------------------
Confirmed 4516 (20.4%)
Partially_confirmed 11570 (52.3%)
Predicted 6030 (27.3%)
Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions 2412 (10.9%)
TrEMBL accessions 18177 (82.2%)
TrEMBLnew accessions 1502 (6.8%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 22091 (99.9%)
Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection 4441
GeneModel correction progress WS108 -> WS109
-----------------------------------------
Confirmed introns not is a CDS gene model;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 1062 | 10 |
St Louis | 750 | -136 |
+---------+--------+
Members of known repeat families that overlap predicted exons;
+---------+--------+
| Introns | Change |
+---------+--------+
Cambridge | 29 | 0 |
St Louis | 31 | 1 |
+---------+--------+
Synchronisation with GenBank / EMBL:
------------------------------------
No synchronisation issues
There are no gaps remaining in the genome sequence
---------------
For more info mail [email protected]
-===================================================================================-
New Data:
---------
A new version of the C.briggsae peptide set will be included (Brigpep2) which is based on the improved gene set.
Brigpep2 will undergo the set of analyses that Wormpep regularly does i.e BLASTP against the various protein sets along with PFAM,
tmhmm etc.
New Fixes:
----------
The new transcript generating / matching_cDNA assignment script incorrectly assigned some OSTs to gene models. This resulted in some genes becoming Partially_confirmed when this was not actually true.This has been remedied hence the slight reduction in the number of Partially_confirmed genes.
Known Problems:
--------------
Other Changes:
--------------
Proposed Changes / Forthcoming Data:
------------------------------------
The next release of WormBase ( WS110 ) will become a "frozen" version, containing several genome sequence corrections.
The BLAT analysis will be upgraded to use the latest version and the post-processing improved. This will probably have little
noticable effect, but should remove many of the poorer quality matches that exist in the database.
-===================================================================================-
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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