WS222

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Release Letter

New release of WormBase WS222, Wormpep222 and Wormrna222 Mon Dec 20 12:07:08 GMT 2010


WS222 was built by Michael Paulini (michael.paulini@wormbase.org)
-===================================================================================-
The WS222 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.WS222.gz  - DNA sequences of all genes confirmed by EST &/or cDNA
     ii) cDNA2orf.WS222.gz         - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
    iii) geneIDs.WS222.gz          - list of all current gene identifiers with CGC & molecular names (when known)
     iv) PCR_product2gene.WS222.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) wormpep222.tar.gz         - full Wormpep distribution corresponding to WS222
    vii) wormrna222.tar.gz         - latest WormRNA release containing non-coding RNA's in the genome
   viii) best_blastp_hits_species.WS222.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.WS222.*.tar.gz   - compressed acedb database for new release
     xi) models.wrm.WS222          - the latest database schema (also in above database files)
    xii) WS222-WS221.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 47376)
------------------------------------------
Molecular_info              45627 (96.3%)
Concise_description         5724 (12.1%)
Reference                   14134 (29.8%)
WormBase_approved_Gene_name 26094 (55.1%)
RNAi_result                 24602 (51.9%)
Microarray_results          22090 (46.6%)
SAGE_transcript             19164 (40.5%)


C. elegans 

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

There are 20424 CDS in autoace, 24938 when counting 4514 alternate splice forms.

The 24938 sequences contain 10,954,721 base pairs in total.

Modified entries      61
Deleted entries       34
New entries           82
Reappeared entries    1

Net change  +49
The differnce between the total CDS's of this (24938) and the last build (24890) does not equal the net change 49
Please investigate! ! 


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

       	WS222       	WS221      	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)
japonica Gene count 27177 (Coding 25870)
briggsae Gene count 23038 (Coding 21967)
brenneri Gene count 32259 (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   3069




-------------------------------------------------
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   5482




-------------------------------------------------
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   4816




-------------------------------------------------
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   5527




-------------------------------------------------
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   3106




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             11743 (47.1%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11020 (44.2%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2175 (8.7%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24749 (99.2%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24749 (99.2%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24468


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 WS222
--------------------------------------

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:  259012

Genes Stats:
----------------
Genes with GO_term connections         86747  
           IEA GO_code present         80723  
       non-IEA GO_code present         6020  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   25788  
        *citace                        2224  
        *Inherited (motif & phenotype) 14421  

GO_terms Stats:
---------------
Total No. GO_terms                     30477  
GO_terms connected to Genes            3287  
GO annotations connected with IEA      1843  
GO annotations connected with non-IEA  1439  
   Breakdown  IC - 3   IDA - 356   ISS - 131 
             IEP - 9   IGI - 116   IMP - 732 
             IPI - 69  NAS - 1     ND  - 1  
             RCA - 0   TAS - 20   


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

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

Genes with Sequence and CGC name
WS222 46468 (24468 elegans / 5527 briggsae / 5482 remanei / 4816 japonica / 3106 brenneri / 3069 pristionchus)


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



New Data:
---------
includes ~21000 mapped C.elegans 3' UTR features from the modENCODE
project.



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


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


Known Problems:
---------------
3-prime UTR mapping data for the ACeDB database is provided as a patch:
ftp://ftp.sanger.ac.uk/pub2/wormbase/WS222/acedb/patches/feature_three_prime_UTR.ace.gz


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

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

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

?Variation tag removal - Mary Ann Tuli
----------------------

Due to a change in how we process CGH alleles there is no longer any need to calculate the 5' and 3' gap
(the gap between the CGH_deleted_probes and Flanking_sequences).

I would therefore like to remove FivePrimeGap & ThreePrimeGap from the ?Variation model.

< FivePrimeGap
< ThreePrimeGap

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.

____________  END _____________

Patches

UTRome mappings

UniProt XRefs

UniProt Xrefs were missing from a lot of Proteins and CDSes. Uniprot is chasing up why they went missing. Meanwhile the UniProt Xrefs of WS221 were used and can be found at ftp://ftp.sanger.ac.uk/pub2/wormbase/WS222/acedb/patches/cds_embl_data.ace.gz

Other new data

WGS data

  • 2722 SNPs identified through WGS by the Gene Knockout Consortium have been submitted to dbSNP. The ss# are included in the WormBase records. The dbSNP records will be available in their next Build (Jan - Mar 2011).