WS147

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Release Letter

New release of WormBase WS147, Wormpep147 and Wormrna147 Thu Aug 18 16:59:45 BST 2005


WS147 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS147.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS147           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS147-WS146.dbcomp         -   log file reporting difference from last release
v)   wormpep147.tar.gz          -   full Wormpep distribution corresponding to WS147
vi)   wormrna147.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS147.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS147.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS147.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS147.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS147.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.WS147.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS147.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS147.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 WS147
------------------------------------
brigdb : 2004-03-12
camace : 2005-08-01 - updated
citace : 2005-07-29 - updated
cshace : 2005-03-07
genace : 2005-08-01 - updated
stlace : 2005-07-29 - updated


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

        WS147           WS146           change
----------------------------------------------
a       32366710        32366710          +0
c       17780361        17780361          +0
g       17756436        17756436          +0
t       32366406        32366406          +0
n       0               0                 +0
-       0               0                 +0

Total   100269913       100269913         +0


Gene data set (Live C.elegans genes 23919)
------------------------------------------
Molecular_info              22111 (92.4%)
Concise_description          4091 (17.1%)
Reference                    4644 (19.4%)
CGC_approved Gene name       8191 (34.2%)
RNAi_result                 19783 (82.7%)
Microarray_results          19118 (79.9%)
SAGE_transcript             18300 (76.5%)




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

There are 20055 CDS in autoace, 22806 when counting 2751 alternate splice forms.

The 22806 sequences contain 10,023,921 base pairs in total.

Modified entries              41
Deleted entries               24
New entries                   28
Reappeared entries             1

Net change  +5



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6445 (28.3%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11414 (50.0%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4947 (21.7%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2945 (12.9%)
TrEMBL accessions     19532 (85.6%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22477 (98.6%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   6449


GeneModel correction progress WS146 -> WS147
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    186  |    -1  |
St Louis        |     82  |   -10  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    593  |    -3  |
St Louis        |    794  |    -5  |
                +---------+--------+



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

CHROMOSOME_I    sequence AL032679
CHROMOSOME_I    sequence AC024206
CHROMOSOME_I    sequence AC024796
CHROMOSOME_I    sequence AF003139
CHROMOSOME_II   sequence AL590344
CHROMOSOME_II   sequence AL032669
CHROMOSOME_II   sequence AF025458
CHROMOSOME_II   sequence AF024493
CHROMOSOME_II   sequence U80453
CHROMOSOME_III  sequence AL031226
CHROMOSOME_III  sequence AF078783
CHROMOSOME_III  sequence AF040660
CHROMOSOME_III  sequence AF099913
CHROMOSOME_IV   sequence AL032676
CHROMOSOME_IV   sequence AC006742
CHROMOSOME_IV   sequence AF067615
CHROMOSOME_IV   sequence AF078781
CHROMOSOME_V    sequence AL031270
CHROMOSOME_V    sequence AF068714
CHROMOSOME_V    sequence AC006744
CHROMOSOME_V    sequence AF101312
CHROMOSOME_X    sequence AL031272
CHROMOSOME_X    sequence AL954368
CHROMOSOME_X    sequence AL954365
CHROMOSOME_X    sequence BX000427

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



New Data:
---------
1) Large increase in Microarray_results due to recent publications.

New Fixes:
----------
1) Variation schema and data was out of sync for WS146, this has been partially 
   resolved for WS147 by grouping Description tags and info under a Pheynotype_remark 
   tag. This will be fully resolved for WS148 as the model is being rolled back while 
   curators get to work representing this data as Phenotype objects.

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


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

Proposed Changes / Forthcoming Data:
------------------------------------
1) New Expression_cluster class to replace Cluster to represent microarray result 
   clusters.

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

1) Expression_cluster model.

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


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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