WS117

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Release Letter

New release of WormBase WS117, Wormpep117 and Wormrna117 Tue Jan 20 10:22:06 GMT 2004


WS117 was built by Paul Davis
======================================================================

This directory includes:
i)      database.WS117.*.tar.gz    -   compressed data for new release
ii)     models.wrm.WS117           -   the latest database schema (also in above database files)
iii)    CHROMOSOMES/subdir        -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)     WS117-WS116.dbcomp          -   log file reporting difference from last release
v)      wormpep117.tar.gz          -   full Wormpep distribution corresponding to WS117
vi)     wormrna117.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)    confirmed_genes.WS117.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)   yk2orf.WS117.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)     gene_interpolated_map_positions.WS117.gz    - Interpolated map positions for each coding/RNA gene
x)      clone_interpolated_map_positions.WS117.gz    - Interpolated map positions for each clone
xi)     best_blastp_hits.WS117.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.WS117.gz   - for each C. briggsae protein, lists Best blastp match to
 
                                        human, fly, yeast, C. elegans, and SwissProt & Trembl proteins.


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS117
------------------------------------
brigdb : 2003-12-02
camace : 2004-01-06 - updated
citace : 2004-01-05 - updated
cshace : 2003-11-26
genace : 2004-01-09 - updated
stlace : 2003-12-02


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

        WS117           WS116           change
----------------------------------------------
a       32368607        32368607          +0
c       17780992        17780992          +0
g       17758424        17758424          +0
t       32369797        32369797          +0
n       95              95                +0
-       0               0                 +0

Total   100277915       100277915         +0




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

There are 19889 CDS in autoace, 22227 when counting 2338 alternate splice forms.

The 22227 sequences contain 9,725,601 base pairs in total.

Modified entries               0
Deleted entries                0
New entries                    0
Reappeared entries             0

Net change  +0



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed           3687 (16.6%)        Every base has transcription evidence (mRNA, EST etc )
Partially_confirmed 12948 (58.3%)       Some but not all bases are covered by transcript evidence
Predicted           5592 (25.2%)        No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2462 (11.1%)
TrEMBL accessions     18489 (83.2%)
TrEMBLnew accessions   1221 (5.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22170 (99.7%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4850


GeneModel correction progress WS116 -> WS117
-----------------------------------------
Confirmed introns not is a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    467  |    35  |
St Louis        |    357  |    56  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |      0  |     0  |
St Louis        |     36  |     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:
---------
There are ~700 new markers displayed on the genetic map.  
These have been entered following correspondence with the CGC and are based on the 
interpolate map positions that have supporting Allele data.

SRX gene family update from Hugh Robertson. The majority has been entered for 
WS117 with the completion in future releases.

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


Known Problems:
--------------
There is a problem regarding the CDS objects not being identified as having the 
correct level of conformation. A high percentage of Confirmed coding CDSs have been 
re-distributed between Partially_confirmed and Predicted.  This should be resolved 
for WS118

BlastP data contains the same data as WS116 but with added analysis data for all
new proteins.

BlastX is the same data as for WS116 for all analysis types but has new wormpep 
data matches.

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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