WS131

From WormBaseWiki
Jump to: navigation, search

Release Letter

New release of WormBase WS131, Wormpep131 and Wormrna131 Tue Sep  7 15:06:49 BST 2004


WS131 was built by Paul Davis
======================================================================

This directory includes:
i)      database.WS131.*.tar.gz    -   compressed data for new release
ii)     models.wrm.WS131           -   the latest database schema (also in above database files)
iii)    CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)     WS131-WS130.dbcomp         -   log file reporting difference from last release
v)      wormpep131.tar.gz          -   full Wormpep distribution corresponding to WS131
vi)     wormrna131.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)    confirmed_genes.WS131.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)   yk2orf.WS131.gz            -   Latest set of ORF connections to each Yuji Kohara EST clone
ix)     gene_interpolated_map_positions.WS131.gz    - Interpolated map positions for each coding/RNA gene
x)      clone_interpolated_map_positions.WS131.gz   - Interpolated map positions for each clone
xi)     best_blastp_hits.WS131.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.WS131.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)   geneIDs.WS131.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)    PCR_product2gene.WS131.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 WS131
------------------------------------
brigdb : 2004-03-12
camace : 2004-08-24 - updated
citace : 2004-08-16 - updated
cshace : 2004-05-10
genace : 2004-09-01 - updated
stlace : 2004-08-16 - updated


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

        WS131           WS130           change
----------------------------------------------
a       32368573        32368573          +0
c       17781252        17781252          +0
g       17758265        17758265          +0
t       32369957        32369957          +0
n       0               0                 +0
-       0               0                 +0

Total   100278047       100278047         +0




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

There are 19766 CDS in autoace, 22297 when counting 2531 alternate splice forms.

The 22297 sequences contain 9,842,631 base pairs in total.

Modified entries              73
Deleted entries               50
New entries                   96
Reappeared entries             1

Net change  +47The differnce between the total CDS's of this (22297) and the last build (22249) does not equal the net change 47
Please investigate! ! 




Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              5615 (25.2%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10919 (49.0%)     Some, but not all exon bases are covered by transcript evidence
Predicted              5763 (25.8%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2711 (12.2%)
TrEMBL accessions     19262 (86.4%)
TrEMBLnew accessions      0 (0.0%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22178 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5214


GeneModel correction progress WS130 -> WS131
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    519  |  -274  |
St Louis        |    209  |  -343  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    604  |    -4  |
St Louis        |    830  |    -1  |
                +---------+--------+



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

CHROMOSOME_II   sequence U39471

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



New Data:
---------
Updated IPI human protein set included in this build.



New Fixes:
----------
Known problems documented in the WS130 release letter have been resolved.

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


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

Proposed Changes / Forthcoming Data:
------------------------------------
SRZ family update.
Update to the ortholog assignments for elegans CDS <-> briggsae CDS.

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


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 _____________