WS163

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Release Letter

New release of WormBase WS163, Wormpep163 and Wormrna163 Thu Aug 17 10:49:02 BST 2006


WS163 was built by Paul Davis [paul.davis@wormbase.org]
======================================================================

This directory includes:
i)   database.WS163.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS163           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS163-WS162.dbcomp         -   log file reporting difference from last release
v)   wormpep163.tar.gz          -   full Wormpep distribution corresponding to WS163
vi)   wormrna163.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS163.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS163.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS163.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS163.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS163.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.WS163.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS163.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS163.gz   - Mappings between PCR products and overlapping Genes


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



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

        WS163           WS162           change
----------------------------------------------
a       32365888        32365888          +0
c       17779857        17779855          +2
g       17756012        17756011          +1
t       32365687        32365687          +0
n       0               0                 +0

Total   100267444       100267441         +3


Chromosomal Changes:
--------------------

Chromosome: III
5953905 5953937 33   ->   5953905 5953940 36

Chromosome: V
20919397 20919396 0   ->   20919397 20919450 54


Gene data set (Live C.elegans genes 23757)
------------------------------------------
Molecular_info              22036 (92.8%)
Concise_description          4223 (17.8%)
Reference                    6322 (26.6%)
CGC_approved Gene name       8835 (37.2%)
RNAi_result                 19804 (83.4%)
Microarray_results          19141 (80.6%)
SAGE_transcript             0 (0%)




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

There are 20071 CDS in autoace, 23164 when counting 3093 alternate splice forms.

The 23164 sequences contain 10,171,003 base pairs in total.

Modified entries              18
Deleted entries                7
New entries                   16
Reappeared entries             0

Net change  +9



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7775 (33.6%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10758 (46.4%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4631 (20.0%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3268 (14.1%)
UniProtKB/TrEMBL accessions     19611 (84.7%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22879 (98.8%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7169


GeneModel correction progress WS162 -> WS163
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |     17  |     0  |
St Louis        |     10  |     5  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |      6  |  -563  |
St Louis        |      6  |  -740  |
                +---------+--------+



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

CHROMOSOME_III  sequence U23172

There are no gaps remaining in the genome sequence
---------------
For more info mail help@wormbase.org
-===================================================================================-



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


New Fixes:
----------
SAGE data has been overhauled to allow the data to be more accessible.

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


Other Changes:
--------------
F25B5: 3 bases were added to resolve sequencing errors in to original sequencing project.


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


Model Changes:
------------------------------------


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


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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