WS169

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Release Letter

New release of WormBase WS169, Wormpep169 and Wormrna169 Fri Dec 22 15:09:52 GMT 2006


WS169 was built by Paul
======================================================================

This directory includes:
i)   database.WS169.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS169           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS169-WS168.dbcomp         -   log file reporting difference from last release
v)   wormpep169.tar.gz          -   full Wormpep distribution corresponding to WS169
vi)   wormrna169.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS169.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS169.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS169.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS169.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS169.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.WS169.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS169.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS169.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:
----------------------------

        WS169           WS168           change
----------------------------------------------
a       32365889        32365889          +0
c       17779856        17779857          -1
g       17756016        17756012          +4
t       32365689        32365686          +3
n       0               0                 +0

Total   100267450       100267444         +6
Total number of bases has increased due to a number of genome sequence changes see notes further down.


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

Chromosome: I
7140372 7140372 1   ->   7140372 7140372 1
13168444 13168443 0   ->   13168444 13168444 1

Chromosome: II
8870302 8870301 0   ->   8870302 8870302 1
10828222 10828222 1   ->   10828223 10828223 1
11864669 11864668 0   ->   11864670 11864670 1

Chromosome: III
3483743 3483742 0   ->   3483743 3483743 1

Chromosome: IV
12082434 12082433 0   ->   12082434 12082434 1
12124684 12124704 21   ->   12124685 12124703 19

Chromosome: V
13100100 13100109 10   ->   13100100 13100111 12
13100695 13100695 1   ->   13100697 13100696 0
16896532 16896531 0   ->   16896533 16896533 1

Chromosome: X
9890865 9890864 0   ->   9890865 9890865 1
11588899 11588899 1   ->   11588900 11588899 0
14847044 14847043 0   ->   14847044 14847044 1


Gene data set (Live C.elegans genes 23964)
------------------------------------------
Molecular_info              22264 (92.9%)
Concise_description          4288 (17.9%)
Reference                    6655 (27.8%)
CGC_approved Gene name       8907 (37.2%)
RNAi_result                 19841 (82.8%)
Microarray_results          19132 (79.8%)
SAGE_transcript             20026 (83.6%)




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

There are 20083 CDS in autoace, 23221 when counting 3138 alternate splice forms.

The 23221 sequences contain 10,183,692 base pairs in total.

Modified entries              32
Deleted entries                2
New entries                   10
Reappeared entries             1

Net change  +9



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              7822 (33.7%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10737 (46.2%)     Some, but not all exon bases are covered by transcript evidence
Predicted              4662 (20.1%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB/Swiss-Prot accessions   3270 (14.1%)
UniProtKB/TrEMBL accessions     19461 (83.8%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            22731 (97.9%)



Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
---------------------------------------------
Entries with CGC-approved Gene name   7261


GeneModel correction progress WS168 -> WS169
-----------------------------------------
Confirmed introns not in a CDS gene model;

                +---------+--------+
                | Introns | Change |
                +---------+--------+
Cambridge       |     15  |     0  |
St Louis        |     11  |     1  |
                +---------+--------+


Members of known repeat families that overlap predicted exons;

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



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

CHROMOSOME_IV   sequence Z68507

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



New Data:
---------
* Incorporation of new SAGE libraries.

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

C27C12   Insertion    attcagcaagctattctagTctctcgactcatacgtcattt
C34B4    Insertion    ttgagtttgatggttcaactgaaatTggtcagtgtc
C34B4    Insertion    ggtcagtgtcTttcttcactttgcctgaaacttgga
C34B4    Deletion     gagaataaacttcattAcctcagatattcctgtt
C34C12   Insertion    gataaatccgacttggcgggGaagttcttgccgccctgg           
F09C6    Insertion    tatccaaaaaaatcctatTtgaaggaagttcagaagctatac
F11A10   Insertion    ttttgaagatgtacactGctttgcagcgacaaatgag
F21G4    Insertion    accattgggaattcccggagGaaaagtgtgatgttttctttaaat
F22G12   Insertion    attccctgaacttcggagcaatCactcatcaacgatcagctcgac
F52D10   Deletion     cacatcacagtatttattcCcaacatcaatctttaacggta
K10D3    Deletion     tatcgagcttgaagtaccgtGttcaattggagcctcagag
K10D3    Insertion    tatcgagcttgaagtaccgtTttcaattggagcctcagag      
K12D12   Insertion    gaaaaatttggcttgggCcacgaatctttctacgggcggt  
M18      Deletion     aatattttacacaatcaccCaatttttatatttatcgttc
M18      Deletion     atttttatatttatcgttcCtactactttcctttctcgtga
T07D4    Insertion    aacctgatcccggcgGgcgttgacgtgcttttaa
VM106R   Deletion     gtcctgatgatggcgagTgatacacgtcgcga
VM106R   Insertion    gtcctgatgatggcgagCgatacacgtcgcga
NET +6

New Fixes:
----------
* Pictar binding sites have been updated as they have been discrepant in past releases.

Known Problems:
---------------
Blast on 

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

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


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

Added ?Homology_group Group_type  UNIQUE OrthoMCL_group for Erich

and

?Gene Orthologue_other  ?Database ?Database_field UNIQUE ?Accession_number ?Species  #Evidence
so that we can connect Ortholog pairs to species outside those that we create ?Gene objects for eg Human

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


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 _____________