WS195

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Release letter

New release of WormBase WS195, Wormpep195 and Wormrna195 Tue Sep 30 09:36:25 BST 2008

WS195 was built by Anthony
======================================================================

This directory includes:
i)   database.WS195.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS195           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS195-WS194.dbcomp         -   log file reporting difference from last release
v)   wormpep195.tar.gz          -   full Wormpep distribution corresponding to WS195
vi)   wormrna195.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS195.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS195.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS195.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS195.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS195.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.WS195.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS195.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS195.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:
----------------------------

           WS195           WS194          change
----------------------------------------------
a        32365950    32365950      +0
c        17779889    17779889      +0
g        17756041    17756041      +0
t        32365753    32365753      +0
n        0           0             +0
-        0           0             +0

Total    100267633    100267633      +0

Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.

Gene data set (Live C.elegans genes 29879)
------------------------------------------
Molecular_info              28159 (94.2%)
Concise_description         5443 (18.2%)
Reference                   13229 (44.3%)
WormBase_approved Gene name 15596 (52.2%)
RNAi_result                 0 (0%)
Microarray_results          20432 (68.4%)
SAGE_transcript             18844 (63.1%)

Wormpep data set:
----------------------------
There are 20198 CDS in autoace, 23906 when counting 3708 alternate splice forms.
The 23906 sequences contain 10,526,596 base pairs in total.

Modified entries      59
Deleted entries       34
New entries           55
Reappeared entries    0

Net change  +21


Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8513 (35.6%)    Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10992 (46.0%)    Some, but not all exon bases are covered by transcript evidence
Predicted              4401 (18.4%)    No transcriptional evidence at all

Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23770 (99.4%)


Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23774 (99.4%)


Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13924

GeneModel correction progress WS194 -> WS195
-----------------------------------------
Confirmed introns not in a CDS gene model;

        +---------+--------+
        | Introns | Change |
        +---------+--------+
Cambridge    |     27  |   -83  |
St Louis     |    103  |   -55  |
        +---------+--------+


Members of known repeat families that overlap predicted exons;

        +---------+--------+
        | Repeats | Change |
        +---------+--------+
Cambridge    |      6  |     0  |
St Louis     |      6  |     0  |
        +---------+--------+



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

CHROMOSOME_I    sequence AC024201
CHROMOSOME_III    sequence U13019
CHROMOSOME_III    sequence AC006605
CHROMOSOME_IV    sequence AF067612
CHROMOSOME_IV    sequence AC025715
CHROMOSOME_X    sequence U41550
CHROMOSOME_X    sequence AC084152

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



New Data:
---------
C.JAPONICA
The C.japonica genome sequence and annotation are included in this release. 
Gene predictions are from the nGASP project.
The standard set proteins sets have been blasted against the genome sequence and proteome.
Protein annotation with PFAM and InterPro domains etc is included.
Orthologies with other nematodes has been determined using the COMPARA analysis method and gene names transfered where appropriate.
C.japonica is also included in the multigenome alignments available from the FTP site.

Genome sequence updates:
-----------------------
NONE

New Fixes:
----------
A problem with CDSs that have more that one coding_transcipt being appearing as non-coding genes in the genome browser has been fixed.  This was patched for WS194


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


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

Proposed Changes / Forthcoming Data:
-------------------------------------
The C.brenneri genome will be included in WS196


Model Changes:
------------------------------------

added confidence info to ?Interaction

fixed typo in ?Strain  Phenotype_info

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


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 _____________

Patches

Inparanoid

available at: [inparanoid_patch]

  • as some C.elegans proteins in the Inparanoid6 XML files errouneoulsy specify Homo sapiens, some "dodgy" human proteins were created
  • the patch should correct the ids, merge them into the C.elegans proteins and fix the Species + EnsEMBL xrefs