WS135

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Release Letter

New release of WormBase WS135, Wormpep135 and Wormrna135 Thu Nov 11 13:32:31 GMT 2004


WS135 was built by Paul Davis
======================================================================

This directory includes:
i)      database.WS135.*.tar.gz    -   compressed data for new release
ii)     models.wrm.WS135           -   the latest database schema (also in above database files)
iii)    CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)     WS135-WS134.dbcomp         -   log file reporting difference from last release
v)      wormpep135.tar.gz          -   full Wormpep distribution corresponding to WS135
vi)     wormrna135.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)    confirmed_genes.WS135.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)   cDNA2orf.WS135.gz            -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)     gene_interpolated_map_positions.WS135.gz    - Interpolated map positions for each coding/RNA gene
x)      clone_interpolated_map_positions.WS135.gz   - Interpolated map positions for each clone
xi)     best_blastp_hits.WS135.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.WS135.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)   geneIDs.WS135.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)    PCR_product2gene.WS135.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 WS135
------------------------------------
brigdb : 2004-03-12
camace : 2004-10-26 - updated
citace : 2004-10-22 - updated
cshace : 2004-10-14 - updated
genace : 2004-10-25 - updated
stlace : 2004-10-25 - updated


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

        WS135           WS134           change
----------------------------------------------
a       32368573        32368573          +0
c       17781252        17781252          +0
g       17758265        17758265          +0
t       32369957        32369957          +0
n       0               0                 +0
-       0               0                 +0

Total   100278047       100278047         +0




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

There are 19719 CDS in autoace, 22338 when counting 2619 alternate splice forms.

The 22338 sequences contain 9,910,260 base pairs in total.

Modified entries              30
Deleted entries               13
New entries                   29
Reappeared entries             1

Net change  +17



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6241 (27.9%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11459 (51.3%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4638 (20.8%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2748 (12.3%)
TrEMBL accessions     19324 (86.5%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22218 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5440


GeneModel correction progress WS134 -> WS135
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    370  |     0  |
St Louis        |     46  |    -6  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    586  |    -8  |
St Louis        |    761  |   -15  |
                +---------+--------+



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:
---------
+Manually curated binding site data taken from publications.

+New Uniprot database released, WormBase has taken this opportunity to revise our 
 protein naming convention from Uniprot IDs to Accession numbers.

             eg. SW:3BP5_MOUSE will now be named Q9Z131

+~300 GFP pictures.

New Fixes:
----------
+Landmark genes back in gff files.

+Oligo_set data is now connected to Coding_transcripts objects to capture instances 
 where the Oligo_set data only overlapped UTR sequence these associations were 
 previously missed.


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

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

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


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


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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