WS223

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Release Letter

 

New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011


WS223 was built by Paul Davis
-===================================================================================-
The WS223 build directory includes:
genomes DIR              -  contains a sub dir for each WormBase species with sequence, gff, and agp data
        genomes/b_malayi:        - genome_feature_tables/       sequences/
        genomes/c_brenneri:      - genome_feature_tables/       sequences/
        genomes/c_briggsae:      - genome_feature_tables/       sequences/
        genomes/c_elegans:       - annotation/  genome_feature_tables/  sequences/
        genomes/c_japonica:      - genome_feature_tables/       sequences/
        genomes/c_remanei:       - genome_feature_tables/       sequences/
        genomes/h_bacteriophora: - genome_feature_tables/       sequences/
        genomes/h_contortus:     - genome_feature_tables/       sequences/
        genomes/m_hapla:         - genome_feature_tables/       sequences/
        genomes/m_incognita:     - sequences/
        genomes/p_pacificus:     - genome_feature_tables/       sequences/
          *annotation/                    - contains additional annotations
      i) confirmed_genes.WS223.gz  - DNA sequences of all genes confirmed by EST &/or cDNA
     ii) cDNA2orf.WS223.gz         - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
    iii) geneIDs.WS223.gz          - list of all current gene identifiers with CGC & molecular names (when known)
     iv) PCR_product2gene.WS223.gz - Mappings between PCR products and overlapping Genes
      v) oligo_mapping.gz           - V 
          *genome_feature_tables/         - contains the main .gff files and supplementary .gff data
          *sequences/                     - contains dna/      protein/  rna/  sub dirs
            sequences/protein           - WormBase protein set for species + history etc.
     vi) wormpep223.tar.gz         - full Wormpep distribution corresponding to WS223
    vii) wormrna223.tar.gz         - latest WormRNA release containing non-coding RNA's in the genome
   viii) best_blastp_hits_species.WS223.gz  - for each C. elegans WormPep protein, lists Best blastp match to
                        human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.
            sequences/dna               - WormBase dna data genomic sequence (raw, soft_masked masked), agp
     ix) intergenic_sequences.dna.gz
            sequences/rna               - WormBase rna gene data.
acedb DIR                -  Everything needed to generate a local copy of the The Primary database
      x) database.WS223.*.tar.gz   - compressed acedb database for new release
     xi) models.wrm.WS223          - the latest database schema (also in above database files)
    xii) WS223-WS222.dbcomp   - log file reporting difference from last release
          *Non_C_elegans_BLASTX/          - This directory contains the blastx data for non-elegans species
                                                    (reduces the size of the main database)
COMPARATIVE_ANALYSIS DIR - compara.tar.bz2 wormpep217_clw.sql.bz2
ONTOLOGY DIR             - gene_associations, obo files for (phenotype GO anatomy) and associated association files


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




C. elegans Synchronisation with GenBank / EMBL:
------------------------------------

No synchronisation issues


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


C. elegans Gene data set (Live C.elegans genes 47388)
------------------------------------------
Molecular_info              45719 (96.5%)
Concise_description         5726 (12.1%)
Reference                   14134 (29.8%)
WormBase_approved_Gene_name 26110 (55.1%)
RNAi_result                 24631 (52%)
Microarray_results          22112 (46.7%)
SAGE_transcript             19172 (40.5%)


C. elegans 

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

There are 20431 CDS in autoace, 24959 when counting 4528 alternate splice forms.

The 24959 sequences contain 10,959,918 base pairs in total.

Modified entries      165
Deleted entries       17
New entries           38
Reappeared entries    7

Net change  +28
The differnce between the total CDS's of this (24959) and the last build (24938) does not equal the net change 28
Please investigate! ! 


C. elegans Genome sequence composition:
----------------------------

        WS223           WS222           change
----------------------------------------------
a       32367418        32367418          +0
c       17780787        17780787          +0
g       17756985        17756985          +0
t       32367086        32367086          +0
n       0               0                 +0
-       0               0                 +0

Total   100272276       100272276         +0


Pristionchus pacificus Genome sequence composition:
----------------------------
 172773083 total
 a 43813958
 c 32811034
 g 32828589
 t 43810996
 - 0
 n 19508506


Caenorhabditis remanei Genome sequence composition:
----------------------------
 145500347 total
 a 42927857
 c 26293828
 g 26276020
 t 42923178
 - 0
 n 7079464


Caenorhabditis japonica Genome sequence composition:
----------------------------
 163282347 total
 a 39053092
 c 25603225
 g 25576971
 t 39126103
 - 0
 n 33922956


Caenorhabditis briggsae Genome sequence composition:
----------------------------
 108478630 total
 a 33004189
 c 19675861
 g 19707411
 t 33049803
 - 0
 n 3041366


Caenorhabditis brenneri Genome sequence composition:
----------------------------
 190487923 total
 a 52239259
 c 32853644
 g 32897666
 t 52181360
 - 0
 n 20315994




Tier II Gene counts
---------------------------------------------
pristionchus Gene count 24216 (Coding 24216)
remanei Gene count 32431 (Coding 31471)
heterorhabditis Gene count 0 (Coding 0)
japonica Gene count 27177 (Coding 25870)
briggsae Gene count 23038 (Coding 21967)
brenneri Gene count 32260 (Coding 30670)
---------------------------------------------




-------------------------------------------------
Pristionchus pacificus Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed               229 (0.9%)      Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    4982 (20.6%)     Some, but not all exon bases are covered by transcript evidence
Predicted             19006 (78.5%)     No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Pristionchus pacificus entries with WormBase-approved Gene name   3077




-------------------------------------------------
Caenorhabditis remanei Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed               956 (3.0%)      Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    5662 (18.0%)     Some, but not all exon bases are covered by transcript evidence
Predicted             24858 (79.0%)     No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis remanei entries with WormBase-approved Gene name   5495




-------------------------------------------------
Caenorhabditis japonica Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              1182 (4.6%)      Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    4974 (19.2%)     Some, but not all exon bases are covered by transcript evidence
Predicted             19714 (76.2%)     No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis japonica entries with WormBase-approved Gene name   4831




-------------------------------------------------
Caenorhabditis briggsae Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed                52 (0.2%)      Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed     856 (3.9%)      Some, but not all exon bases are covered by transcript evidence
Predicted             21083 (95.9%)     No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  21703 (98.7%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis briggsae entries with WormBase-approved Gene name   5542




-------------------------------------------------
Caenorhabditis brenneri Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              1512 (4.9%)      Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    5635 (18.4%)     Some, but not all exon bases are covered by transcript evidence
Predicted             23526 (76.7%)     No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis brenneri entries with WormBase-approved Gene name   3119




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             11759 (47.1%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11022 (44.2%)     Some, but not all exon bases are covered by transcript evidence
Predicted              2178 (8.7%)      No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24602 (98.6%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24760 (99.2%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24486


C. elegans Operons Stats
---------------------------------------------
Description: These exist as closely spaced gene clusters similar to bacterial operons
---------------------------------------------
| Live Operons        1288                |
| Genes in Operons    3342                |
---------------------------------------------


GO Annotation Stats WS223
--------------------------------------

GO_codes - used for assigning evidence
--------------------------------------
IC  Inferred by Curator
IDA Inferred from Direct Assay
IEA Inferred from Electronic Annotation
IEP Inferred from Expression Pattern
IGI Inferred from Genetic Interaction
IMP Inferred from Mutant Phenotype
IPI Inferred from Physical Interaction
ISS Inferred from Sequence (or Structural) Similarity
NAS Non-traceable Author Statement
ND  No Biological Data available
RCA Inferred from Reviewed Computational Analysis
TAS Traceable Author Statement
------------------------------------------------

Total number of Gene::GO connections:  259979

Genes Stats:
----------------
Genes with GO_term connections         87264  
           IEA GO_code present         81404  
       non-IEA GO_code present         5856  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   24450  
        *citace                        2224  
        *Inherited (motif & phenotype) 15098  

GO_terms Stats:
---------------
Total No. GO_terms                     30478  
GO_terms connected to Genes            3298  
GO annotations connected with IEA      1856  
GO annotations connected with non-IEA  1437  
   Breakdown  IC - 3   IDA - 356   ISS - 130 
             IEP - 9   IGI - 116   IMP - 732 
             IPI - 69  NAS - 1     ND  - 1  
             RCA - 0   TAS - 20   


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

Useful Stats:
---------

Genes with Sequence and CGC name
WS223 46550 (24486 elegans / 5542 briggsae / 5495 remanei / 4831 japonica / 3119 brenneri / 3077 pristionchus)


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



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

Details of 775 wild isolate strains stored at the Felix lab have been curated.
This is the first of such datasets and we continue to work on incorporating
information about wild isolate strains stored in other worm laboratories.
Specific isolation information is included.



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


New Fixes:
----------
Phenotypes "Not" observed: 
The Phenotype observed NOT data model has been retired as this proved confusing to our users. 

Old
Phenotype     "WBPhenotype:0000216" Not 

New
Phenotype_not_observed     "WBPhenotype:0000216" Remark "AC\/VU specification normal" 



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


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

Caenorhabditis sp. 3 PS1010 is now Caenorhabditis angaria.
WormBase will be working to accommodate this change on our ftp and www sites.

http://www.ingentaconnect.com/content/brill/nemy/2011/00000013/00000001/art00007


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

WS224 will include over 20,000 new SNPs from WGS. The data was published in PMID
20439776 Sarin S et al. (2010) Genetics "Analysis of multiple ethyl
methanesulfonate-mutagenized Caenorhabditis ...."
This data has also been submitted to dbSNP.

We are expecting to see a massive increase in this sort of data. 


WS224 will contain the new cb4 C. briggsae assembly.
This will require the revision of any gene model that overlaps the 
rearrangements in the assembly.



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

Simple additions were made to the Transposon_family and Strain classes

The Picture class was substantially re-worked

Small additional changes that should have gone in before.

Additional information can be found here: http://wiki.wormbase.org/index.php/WS223_Models.wrm


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


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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