WS154

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Release Letter

New release of WormBase WS154, Wormpep154 and Wormrna154 Fri Feb 10 12:46:08 GMT 2006


WS154 was built by Paul Davis
======================================================================

This directory includes:
i)   database.WS154.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS154           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS154-WS153.dbcomp         -   log file reporting difference from last release
v)   wormpep154.tar.gz          -   full Wormpep distribution corresponding to WS154
vi)   wormrna154.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS154.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS154.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS154.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS154.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS154.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.WS154.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS154.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS154.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 WS154
------------------------------------
brigdb : 2004-03-12
camace : 2006-01-23 - updated
citace : 2006-01-20 - updated
cshace : 
genace : 2006-01-23 - updated
stlace : 2006-01-20 - updated


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

        WS154           WS153           change
----------------------------------------------
a       32365775        32365775          +0
c       17779813        17779813          +0
g       17755968        17755968          +0
t       32365578        32365578          +0
n       0               0                 +0
-       0               0                 +0

Total   100267134       100267134         +0


Gene data set (Live C.elegans genes 23707)
------------------------------------------
Molecular_info              21956 (92.6%)
Concise_description          4131 (17.4%)
Reference                    4885 (20.6%)
CGC_approved Gene name       8710 (36.7%)
RNAi_result                 19780 (83.4%)
Microarray_results          19108 (80.6%)
SAGE_transcript             18197 (76.8%)




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

There are 20060 CDS in autoace, 22943 when counting 2883 alternate splice forms.

The 22943 sequences contain 10,080,578 base pairs in total.

Modified entries              79
Deleted entries               40
New entries                   82
Reappeared entries             0

Net change  +42



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              6584 (28.7%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11410 (49.7%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4949 (21.6%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3139 (13.7%)
UniProtKB/TrEMBL accessions     19577 (85.3%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22716 (99.0%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7021


GeneModel correction progress WS153 -> WS154
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    126  |   -10  |
St Louis        |      7  |     1  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    585  |    -5  |
St Louis        |    761  |    -3  |
                +---------+--------+



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:
---------
1) Vancouver (VRM) Fosmid library is now mapped to the current elegans assembly and 
   will be available to view in the genome browser.

2) 1215 new RNAi objects.

3) >500 new variations.

New Fixes:
----------
1) Mitochondrial gene predictions will now display correctly within wormbase 
   and the genome browser.
   
   gff is available for all CDSs/Coding_Transcripts/WBgene_spans.
2) The clone C24G6 had incorrect wublastx data in the previous release of WormBase
   (WS153) this has now been resolved.

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


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

Proposed Changes / Forthcoming Data:
------------------------------------
1) Gene -> WRM Fosmid library connections will be generated to speed up 
   fosmid identification.

Model Changes:
------------------------------------
1) Removed Interpolated_map_position from ?CDS, ?Transcript and ?Pseudogene.  
2) Changed ?Variation Interpolated_map_position to be same structure and ?Gene ie
   Interpolated_map_position UNIQUE ?Map UNIQUE Float

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


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 _____________