WS127

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Release Letter

New release of WormBase WS127, Wormpep127 and Wormrna127 Tue Jul  6 13:12:51 BST 2004


WS127 was built by Paul Davis
======================================================================

This directory includes:
i)      database.WS127.*.tar.gz    -   compressed data for new release
ii)     models.wrm.WS127           -   the latest database schema (also in above database files)
iii)    CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)     WS127-WS126.dbcomp         -   log file reporting difference from last release
v)      wormpep127.tar.gz          -   full Wormpep distribution corresponding to WS127
vi)     wormrna127.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)    confirmed_genes.WS127.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii)   yk2orf.WS127.gz            -    Latest set of ORF connections to each Yuji Kohara EST clone
ix)     gene_interpolated_map_positions.WS127.gz    - Interpolated map positions for each coding/RNA gene
x)      clone_interpolated_map_positions.WS127.gz    - Interpolated map positions for each clone
xi)     best_blastp_hits.WS127.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.WS127.gz   - for each C. briggsae protein, lists Best blastp match to
 
                                        human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii)   geneIDs.WS127.gz   - list of all current gene identifiers with CGC & molecular names (when known)


Release notes on the web:
-------------------------
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE



Primary databases used in build WS127
------------------------------------
brigdb : 2004-03-12
camace : 2004-06-23 - updated
citace : 2004-06-17 - updated
cshace : 2004-05-10
genace : 2004-06-24 - updated
stlace : 2004-06-21 - updated


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

        WS127           WS126           change
----------------------------------------------
a       32368573        32368574          -1
c       17781252        17781251          +1
g       17758265        17758269          -4
t       32369957        32369958          -1
n       0               1                 -1
-       0               0                 +0

Total   100278047       100278053         -6
Total number of bases has decreased - please investigate ! 




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

There are 19775 CDS in autoace, 22151 when counting 2376 alternate splice forms.

The 22151 sequences contain 9,776,629 base pairs in total.

Modified entries             124
Deleted entries               89
New entries                   12
Reappeared entries             0

Net change  -77



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              5484 (24.8%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11140 (50.3%)     Some, but not all exon bases are covered by transcript evidence
Predicted              5527 (25.0%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
Swissprot accessions   2599 (11.7%)
TrEMBL accessions     18349 (82.8%)
TrEMBLnew accessions    996 (4.5%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            21951 (99.1%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   5149


GeneModel correction progress WS126 -> WS127
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |    624  |  -122  |
St Louis        |    492  |  -114  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

                +---------+--------+
                | Repeats | Change |
                +---------+--------+
Cambridge       |    621  |   -58  |
St Louis        |    872  |  -117  |
                +---------+--------+



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

CHROMOSOME_II   sequence U39471
CHROMOSOME_II   sequence Z46676

There are no gaps remaining in the genome sequence
--------------------------------------------------

For more info mail help@wormbase.org
-===================================================================================-



New Data:
---------
i)   Wormpep now contains WBGene ID's in the header lines of all peptide sequences.

ii)  Indroduction of Coding Transcripts for all Live genes. Coding Transcripts will 
     also exist to represent UTR isoforms, these will have a new nomenclature 
     eg. CDS:Y106G6D.8 has 2 coding transcripts 
                       Coding_transcript:Y106G6D.8.1 - SL1 Trans-spliced.
                       Coding_transcript:Y106G6D.8.2 - 5'extension as not SL1 Trans-spliced.

iii) Introduction of "Gene Spans" available in the .gff files, these span the known 
     extent of genes. This encompases (CDS/Pseudogene/Transcript), UTR, and feature 
     data associated with each gene.

iv)  Repeat masked chromosomes are available on the ftp site. 
            CHROMOSOME_I_masked.dna.gz
            CHROMOSOME_II_masked.dna.gz
            CHROMOSOME_III_masked.dna.gz
            CHROMOSOME_IV_masked.dna.gz
            CHROMOSOME_V_masked.dna.gz
            CHROMOSOME_X_masked.dna.gz
            

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


Known Problems:
--------------
We are attempting to refine the process of blatting Transcript (EST, OST and mRNA)
sequences back to the genome.  We have noticed that in some cases if there is a 
sequencing error in the Transcript close to an intron/exon boundary, BLAT will attempt 
to find a better hit for a small section of the Transcript away from the real match.  
This results in the production of falsely confirmed introns that are not incorporated 
into gene predictions.  Some of the new Coding_transcript do however contain these 
false introns.  We are working on a method of screening out these false small matches.

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

Proposed Changes / Forthcoming Data:
------------------------------------
i)  Gene spans will be available in the full database with the release of WS128.

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


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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