WS212

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Contents

Release Notes

New release of WormBase WS212, Wormpep212 and Wormrna212 Mon Mar  1 11:51:04 GMT 2010


WS212 was built for the last time by Anthony
======================================================================

This directory includes:
i)   database.WS212.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS212           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS212-WS211.dbcomp         -   log file reporting difference from last release
v)   wormpep212.tar.gz          -   full Wormpep distribution corresponding to WS212
vi)   wormrna212.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS212.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS212.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS212.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS212.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS212.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.WS212.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS212.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS212.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:
----------------------------

        WS212           WS211           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 40094)
------------------------------------------
Molecular_info              38395 (95.8%)
Concise_description         5629 (14%)
Reference                   13813 (34.5%)
WormBase_approved Gene name 25864 (64.5%)
RNAi_result                 24189 (60.3%)
Microarray_results          21069 (52.5%)
SAGE_transcript             19097 (47.6%)




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

There are 20295 CDS in autoace, 24362 when counting 4067 alternate splice forms.

The 24362 sequences contain 10,761,760 base pairs in total.

Modified entries      41
Deleted entries       29
New entries           86
Reappeared entries    1


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              9957 (40.9%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11643 (47.8%)     Some, but not all exon bases are covered by transcript evidence
Predicted              2762 (11.3%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24212 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24212 (99.4%)


Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24213

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

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:
-------------------------------------


Model Changes:
------------------------------------
Changed ?Rearrangement so that Transgene and Variation markers can be included
XREFs made in those classes.

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


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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