WS199

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Release Letter

New release of WormBase WS199, Wormpep199 and Wormrna199 Tue Feb  3 12:09:54 GMT 2009


WS199 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS199.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS199           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS199-WS198.dbcomp         -   log file reporting difference from last release
v)   wormpep199.tar.gz          -   full Wormpep distribution corresponding to WS199
vi)   wormrna199.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome vii)  confirmed_genes.WS199.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS199.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS199.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS199.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS199.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.WS199.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS199.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS199.gz   - Mappings between PCR products and overlapping Genes 

Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



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

        WS199           WS198           change
----------------------------------------------
a       32367419        32367419          +0
c       17780761        17780761          +0
g       17756942        17756942          +0
t       32367086        32367086          +0
n       0               0                 +0
-       0               0                 +0

Total   100272208       100272208         +0


Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.


Gene data set (Live C.elegans genes 39873)
------------------------------------------
Molecular_info              35563 (89.2%)
Concise_description         5528 (13.9%)
Reference                   13340 (33.5%)
WormBase_approved Gene name 25705 (64.5%)
RNAi_result                 22052 (55.3%)
Microarray_results          20729 (52%)
SAGE_transcript             18847 (47.3%)




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

There are 20178 CDS in autoace, 23973 when counting 3795 alternate splice forms.

The 23973 sequences contain 10,572,960 base pairs in total.

Modified entries      26
Deleted entries       25
New entries           35

Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8698 (36.3%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11721 (48.9%)     Some, but not all exon bases are covered by transcript evidence
Predicted              3554 (14.8%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23850 (99.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23850 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  21444


GeneModel correction progress WS198 -> WS199
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |     32  |    -3  |
St Louis        |     89  |     0  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |      6  |     0  |
St Louis        |      6  |     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:
---------


Genome sequence updates:
-----------------------


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
The next release of WormBase will be WS200, a frozen release.  It is anticipated that this will be the reference release to be used for the
analysis paper describing the five currently sequenced Caenorhabditis genomes.

Model Changes:
------------------------------------
added tags to Sequence for short read clusters.
Changed ?Analysis to have standard DB_info line
-===================================================================================-


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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