WS112

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Release Letter

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 help@wormbase.org
-===================================================================================-



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
wormbase-help@wormbase.org

-===================================================================================-


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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