WS142

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Release Letter

New release of WormBase WS142, Wormpep142 and Wormrna142 Fri Apr 15 18:22:51 BST 2005


WS142 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS142.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS142           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS142-WS141.dbcomp         -   log file reporting difference from last release
v)   wormpep142.tar.gz          -   full Wormpep distribution corresponding to WS142
vi)   wormrna142.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS142.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS142.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS142.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS142.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS142.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.WS142.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS142.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS142.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 WS142
------------------------------------
brigdb : 2004-03-12
camace : 2005-03-29 - updated
citace : 2005-03-25 - updated
cshace : 2005-03-07
genace : 2005-03-29 - updated
stlace : 2005-03-25 - updated


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

        WS142           WS141           change
----------------------------------------------
a       32366710        32365928        +782
c       17780361        17779940        +421
g       17756435        17756857        -422
t       32366406        32367188        -782
n       0               0                 +0
-       0               0                 +0

Total   100269912       100269913         -1 


Gene data set (Live C.elegans genes 23624)
------------------------------------------
Molecular_info              21816 (92.3%)
Concise_description          3933 (16.6%)
Reference                    4106 (17.3%)
CGC_approved Gene name       7658 (32.4%)
RNAi_result                 19707 (83.4%)
Microarray_results          18255 (77.2%)
SAGE_transcript             18312 (77.5%)


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

There are 19851 CDS in autoace, 22608 when counting 2757 alternate splice forms.

The 22608 sequences contain 10,006,658 base pairs in total.

Modified entries              45
Deleted entries               39
New entries                  209
Reappeared entries             2

Net change  +172



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6389 (28.3%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11470 (50.7%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4749 (21.0%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions  21146 (93.5%)
TrEMBL accessions        13 (0.1%)
TrEMBLnew accessions      3 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21219 (93.9%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5917


GeneModel correction progress WS141 -> WS142
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    178  |   -77  |
St Louis        |     30  |    -8  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    613  |    40  |
St Louis        |    847  |    75  |
                +---------+--------+



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

CHROMOSOME_I    sequence AF067211
CHROMOSOME_I    sequence AF067211
CHROMOSOME_I    sequence AF067211
CHROMOSOME_X    sequence Z92839

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



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

A)The Genome sequence has changed for WS142:
    1)T08D2 has been inverted to resolve a missasenbly.
    2)C14B9 has a single deletion following a sequence error correction.

B)Some of the RNAi datasets (including the latest set from Tony Hyman) have multiple 
  RNAi mappings to indicate primary and secondary placing on the genome. This allows 
  WormBase to better indicate RNAi experiments which interfere with multipletargets in 
  the genome.

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


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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