WS190

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Release Notes

New release of WormBase WS190, Wormpep190 and Wormrna190 Fri Apr 25 11:03:36 BST 2008


WS190 was built by Anthony
======================================================================

This directory includes:
i)   database.WS190.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS190           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS190-WS189.dbcomp         -   log file reporting difference from last release
v)   wormpep190.tar.gz          -   full Wormpep distribution corresponding to WS190
vi)   wormrna190.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS190.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS190.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS190.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS190.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS190.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.WS190.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS190.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS190.gz   - Mappings between PCR products and overlapping Genes


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



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

        WS190           WS189           change
----------------------------------------------
a       32365950        32365950          +0
c       17779890        17779890          +0
g       17756040        17756040          +0
t       32365752        32365752          +0
n       0               0                 +0
-       0               0                 +0

Total   100267632       100267632         +0


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




Gene data set (Live C.elegans genes 29802)
------------------------------------------
Molecular_info              28107 (94.3%)
Concise_description         5308 (17.8%)
Reference                   7700 (25.8%)
WormBase_approved Gene name 15262 (51.2%)
RNAi_result                 20797 (69.8%)
Microarray_results          20462 (68.7%)
SAGE_transcript             18839 (63.2%)




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

There are 20177 CDS in autoace, 23771 when counting 3594 alternate splice forms.

The  sequences contain 10,449,259 base pairs in total.

Modified entries      71
Deleted entries       27
New entries           68
Reappeared entries    0

Net change  +41

Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8418 (35.4%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10964 (46.1%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4389 (18.5%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23622 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23625 (99.4%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13617

GeneModel correction progress WS189 -> WS190
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |     57  |    -9  |
St Louis        |    165  |    46  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |      6  |     1  |
St Louis        |      6  |     1  |
                +---------+--------+



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

CHROMOSOME_II   sequence U40030

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



New Data:
---------
Uniprot databases update to Knowledgebase major release 13.  This now includes Brugia malayi proteins.
IPI_human blast database has been updated.

All blast and transcript alignments have been update for C.briggsae and C.remanei


Genome sequence updates:
-----------------------


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


Known Problems:
---------------
The automated coding_transcript building code does not currently work with C.remanei so these CDSs do not have UTRs


Other Changes:
--------------
The methods for running blastx have changed slightly due to updating to the latest version of the Ensembl schema/code.
Rather than using the sequenced cosmids as units of sequence to blast against, sequencial 75kb chunks are used.
This has meant we have had to add the parameter hspsepsmax=7500. see http://blast.wustl.edu/blast/parameters.html#hspsepsmax for details.


Proposed Changes / Forthcoming Data:
-------------------------------------


Model Changes:
------------------------------------
Added tags to ?Feature to connect to ?Operon, ?Gene_regulation and ?Expr_pattern

Connected ?Rearrangement to ?Phenotype

Changed Phenotype to Legacy_information in ?Gene to avoid confussion

Updates to ?Neurodata and ?Neuro_location


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


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

Molecular Changes Patches

  • some missense/nonsense molecular changes were wrong. patch files are available from Sanger (apply in order):

Twinscan Prediction Patch

The coordinates of the Twinscan predictions were wrong. A patch can be picked up from Sanger at: Twinscan Patch

additional low complexity features

I created additional RepeatMasker low-complexity features (per user feedback) which are available as: