WormBase release WS141 now online

This is an automatic announcement that WormBase
(http://www.wormbase.org) has just been updated.  New releases occur
roughly every three 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/
   or
   ftp://ftp.wormbase.org/pub/wormbase/elegans/current_release

New release of WormBase WS141, Wormpep141 and Wormrna141 Wed Mar 23 16:18:12 
GMT 2005


WS141 was built by Mary Ann
======================================================================

This directory includes:
i)      database.WS141.*.tar.gz    -   compressed data for new release
ii)     models.wrm.WS141           -   the latest database schema (also in 
above database files)
iii)    CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per 
chromosome)
iv)     WS141-WS140.dbcomp         -   log file reporting difference from last 
release
v)      wormpep141.tar.gz          -   full Wormpep distribution corresponding 
to WS141
vi)     wormrna141.tar.gz          -   latest WormRNA release containing 
non-coding RNA's in the genome
vii)    confirmed_genes.WS141.gz   -   DNA sequences of all genes confirmed by 
EST &/or cDNA
viii)   cDNA2orf.WS141.gz            -   Latest set of ORF connections to each 
cDNA (EST, OST, mRNA)
ix)     gene_interpolated_map_positions.WS141.gz    - Interpolated map 
positions for each coding/RNA gene
x)      clone_interpolated_map_positions.WS141.gz   - Interpolated map 
positions for each clone
xi)     best_blastp_hits.WS141.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.WS141.gz   - for each C. briggsae protein, 
lists Best blastp match to
                                     human, fly, yeast, C. elegans, and 
SwissProt & TrEMBL proteins.
xiii)   geneIDs.WS141.gz   - list of all current gene identifiers with CGC & 
molecular names (when known)
xiv)    PCR_product2gene.WS141.gz   - Mappings between PCR products and 
overlapping Genes


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS141
------------------------------------
brigdb : 2004-03-12
camace : 2005-03-08 - updated
citace : 2005-03-04 - updated
cshace : 2005-03-07 - updated
genace : 2005-03-08 - updated
stlace : 2005-03-04 - updated


Genome sequence composition:
----------------------------

        WS141           WS140           change
----------------------------------------------
a       32365928        32368572        -2644
c       17779940        17781252        -1312
g       17756857        17758265        -1408
t       32367188        32369957        -2769
n       0               0                 +0
-       0               0                 +0

Total   100269913       100278046       -8133


Gene data set (Live C.elegans genes 23569)
------------------------------------------
Molecular_info              21669 (91.9%)
Concise_description          3921 (16.6%)
Reference                    4099 (17.4%)
CGC_approved Gene name       7651 (32.5%)
RNAi_result                 16508 (70.0%)
Microarray_results          18236 (77.4%)
SAGE_transcript             18313 (77.7%)


Wormpep data set:
----------------------------

There are 19729 CDS in autoace, 22436 when counting 2707 alternate splice forms.

The 22436 sequences contain 9,957,916 base pairs in total.

Modified entries             100
Deleted entries               42
New entries                   57
Reappeared entries             1

Net change  +16



Status of entries: Confidence level of prediction (based on the amount of 
transcript evidence)
-------------------------------------------------
Confirmed              6342 (28.3%)     Every base of every exon has 
transcription evidence (mRNA, EST etc.)
Partially_confirmed   11444 (51.0%)     Some, but not all exon bases are 
covered by transcript evidence
Predicted              4650 (20.7%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions  21452 (95.6%)
TrEMBL accessions         4 (0.0%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21493 (95.8%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5906


GeneModel correction progress WS140 -> WS141
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    255  |    -6  |
St Louis        |     38  |     2  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    573  |    -6  |
St Louis        |    772  |     2  |
                +---------+--------+



Synchronisation with GenBank / EMBL:
------------------------------------

No synchronisation issues


There are no gaps remaining in the genome sequence
---------------
For more info mail worm@xxxxxxxxxxxx
-===================================================================================-



New Data:
---------

Incorporation of the latest RNAi data set from Tony Hyman (21,300 experiments)


New Fixes:
----------


Known Problems:
--------------


Other Changes:
--------------

Genome sequence modified to remove an 8.1 kb duplicated region on chromosome I.


Proposed Changes / Forthcoming Data:
------------------------------------

RNAi mappings to indicate primary and secondary placing on the genome. This will
allow WormBase to better indicate RNAi experiments which interfere with multiple
targets in the genome.

New gene predictions based on analysis of novel Genefinder and Twinscan 
predictions.

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


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 _____________