WS122

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Release Letter

New release of WormBase WS122, Wormpep122 and Wormrna122  March 26th 2004


WS122 was built by Paul
======================================================================

This directory includes:
i)    database.WS122.*.tar.gz                   - compressed data for new release
ii)   models.wrm.WS122                          - the latest database schema (also in above database files)
iii)  CHROMOSOMES/subdir                        - contains 3 files (DNA, GFF & AGP per chromosome)
iv)   WS122-WS121.dbcomp                        - log file reporting difference from last release
v)    wormpep122.tar.gz                         - full Wormpep distribution corresponding to WS122
vi)   wormrna122.tar.gz                         - latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS122.gz                  - DNA sequences of all genes confirmed by EST &/or cDNA
viii) yk2orf.WS122.gz                           - Latest set of ORF connections to each Yuji Kohara EST clone
ix)   gene_interpolated_map_positions.WS122.gz  - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS122.gz - Interpolated map positions for each clone
xi)   best_blastp_hits.WS122.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.WS122.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 WS122
------------------------------------
brigdb : 2004-03-12 - updated
camace : 2004-03-15 - updated
citace : 2004-03-14 - updated
cshace : 2004-03-03 - updated
genace : 2004-03-19 - updated
stlace : 2004-03-12 - updated


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

        WS122           WS121           change
----------------------------------------------
a       32368547        32368547          +0
c       17781234        17781234          +0
g       17758249        17758249          +0
t       32369937        32369937          +0
n       8               8                 +0
-       0               0                 +0

Total   100277975       100277975         +0




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

There are 19895 CDS in autoace, 22264 when counting 2369 alternate splice forms.

The 22264 sequences contain 9,767,313 base pairs in total.

Modified entries              45
Deleted entries                9
New entries                   12
Reappeared entries             7

Net change  +10



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              4870 (21.9%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   12049 (54.1%)     Some, but not all exon bases are covered by transcript evidence
Predicted              5345 (24.0%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2425 (10.9%)
TrEMBL accessions     18443 (82.8%)
TrEMBLnew accessions   1236 ( 5.6%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22212 (99.8%)



Locus <-> Sequence connections (cgc-approved)
---------------------------------------------
Entries with locus connection   4973


GeneModel correction progress WS121 -> WS122
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    419  |   -10  |
St Louis        |    278  |    19  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    662  |   662  |
St Louis        |   1028  |  1028  |
                +---------+--------+



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

CHROMOSOME_II   sequence Z46676

There are no gaps remaining in the genome sequence

For more info mail help@wormbase.org

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



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

The SAGE analysis from Jones et al has been incorporated into this release. There
are approximately 35,000 SAGE tags in the dataset. 

Marker loci on the genetic map have been partioned into those which have been
experimentally defined (displayed in yellow) and those which are computationally
inferred (displayed in orange).



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


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


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

The script that check overlaps between coding exons and repeat sequences now uses
the RepeatMasker data. Hence, the numbers have increased significantly. There are
two caveats to these numbers; Firstly, at the moment these include the low-complexity
mark up of RepeatMasker which we will in future ignore, this will reduce the numbers 
by approximately a third. Secondly, the latest RepeatMasker library still contains
some motifs from multiple-gene families and hence overestimates the number of genes
which need attention. The curators will work through this list to remove these motifs
from the repeat library.

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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