WS214

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New release of WormBase WS214, Wormpep214 and Wormrna214 Tue Apr 27 15:37:39 BST 2010


WS214 was built by gw3
======================================================================

This directory includes:
i)   database.WS214.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS214           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS214-WS213.dbcomp         -   log file reporting difference from last release
v)   wormpep214.tar.gz          -   full Wormpep distribution corresponding to WS214
vi)   wormrna214.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS214.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS214.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS214.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS214.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS214.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.WS214.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS214.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS214.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:
----------------------------

        WS214           WS213           change
----------------------------------------------
a       32367418        32367418          +0
c       17780763        17780763          +0
g       17756943        17756943          +0
t       32367086        32367086          +0
n       0               0                 +0
-       0               0                 +0

Total   100272210       100272210         +0


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


Gene data set (Live C.elegans genes 40147)
------------------------------------------
Molecular_info              38450 (95.8%)
Concise_description         5658 (14.1%)
Reference                   13883 (34.6%)
WormBase_approved Gene name 25913 (64.5%)
RNAi_result                 24209 (60.3%)
Microarray_results          21070 (52.5%)
SAGE_transcript             19108 (47.6%)




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

There are 20337 CDS in autoace, 24575 when counting 4238 alternate splice forms.

The 24575 sequences contain 10,847,777 base pairs in total.

Modified entries      41
Deleted entries       21
New entries           85
Reappeared entries    4

Net change  +68




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             10092 (41.1%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11756 (47.8%)     Some, but not all exon bases are covered by transcript evidence
Predicted              2727 (11.1%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24410 (99.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24410 (99.3%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24264


GeneModel correction progress WS213 -> WS214
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |      0  |     0  |
St Louis        |      0  |     0  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

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

Blast databases updated:
 IPI_human
 Yeast
 Flybase

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

None.

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

None.

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

None.

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

There are now no instances of the Journal class used.

Changes to the miRNA class with both Primary and Mature annotations


Variation objects now have a controlled ID of the form: 'WBVar00000001'


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

WS215:

Revert Transgene phenotype-gene link but added to Phenotype_info hash. Added Species to Rearrangement

Added NBCI tax id to ?Species

Removed ?Journal class

Added Tags for grouping ?Analysis objects

Added Sex, Food and duration info to ?Condition

Added Species to ?Rearrangement


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


Revert Transgene phenotype-gene link but added to Phenotype_info hash. Added Species to Rearrangement



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


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 _____________