WS201

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Release letter

New release of WormBase WS201, Wormpep201 and Wormrna201 Wed Mar 25 15:30:27 GMT 2009


WS201 was built by Michael Han (mh6@sanger.ac.uk)
======================================================================

This directory includes:
i)   database.WS201.*.tar.gz    - compressed data for new release
ii)  models.wrm.WS201           - the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         - contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS201-WS200.dbcomp         - log file reporting difference from last release
v)   wormpep201.tar.gz          - full Wormpep distribution corresponding to WS201
vi)   wormrna201.tar.gz         - latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS201.gz  - DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS201.gz         - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS201.gz  - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS201.gz - Interpolated map positions for each clone
xi)   best_blastp_hits.WS201.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.WS201.gz - for each C. briggsae protein, lists Best blastp match to
                                           human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS201.gz          - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS201.gz - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



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

        WS201           WS200       change
----------------------------------------------
a       32367418    32367419      -1
c       17780761    17780761      +0
g       17756943    17756942      +1
t       32367086    32367086      +0
n       0           0             +0
-       0           0             +0

Total   100272208   100272208     +0


Chromosomal Changes:
--------------------

Chromosome: II
10864074 10864074 1   ->   10864074 10864073 0

Chromosome: III
4074142  4074142  1   ->   4074142  4074141  0
9322815  9322814  0   ->   9322814  9322814  1
10505397 10505402 6   ->   10505397 10505403 7


Gene data set (Live C.elegans genes 39873)
------------------------------------------
Molecular_info              35561 (89.2%)
Concise_description         5552  (13.9%)
Reference                   13428 (33.7%)
WormBase_approved Gene name 25753 (64.6%)
RNAi_result                 22047 (55.3%)
Microarray_results          20722 (52%)
SAGE_transcript             18863 (47.3%)




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

There are 20171 CDS in autoace, 23993 when counting 3822 alternate splice forms.

The 23993 sequences contain 10,589,685 base pairs in total.

Modified entries      40
Deleted entries       13
New entries           34
Reappeared entries    1

Net change  +22


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8715 (36.3%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11727 (48.9%) Some, but not all exon bases are covered by transcript evidence
Predicted              3551 (14.8%) No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23872 (99.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23872 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  21490


GeneModel correction progress WS200 -> WS201
-----------------------------------------
Confirmed introns not in a CDS gene model;

          +---------+--------+
          | Introns | Change |
          +---------+--------+
Cambridge |      0  |     0  |
St Louis  |      0  |     0  |
          +---------+--------+


Members of known repeat families that overlap predicted exons;

            +---------+--------+
            | Repeats | Change |
            +---------+--------+
Cambridge   |      0  |     0  |
St Louis    |      0  |     0  |
            +---------+--------+



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

CHROMOSOME_II   sequence Z46935
CHROMOSOME_III  sequence Z38112
CHROMOSOME_III  sequence Z19154
CHROMOSOME_III  sequence Z35640

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

C.elegans was updated
C.remanei was updated
P.pacificus was updated

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


Genome sequence updates:
-----------------------
four genomic sequences fixes were made based on user feedback and re-examination of the
underlying traces.


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


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
TreeFam 7 data import

Model Changes:
------------------------------------
no changes between WS200 and WS201

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


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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