WS228

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Release Notes

New release of WormBase WS228

WS228 was built by Paul Davis
-===================================================================================-
The WS228 build directory includes:
species/ DIR              -  contains a sub dir for each WormBase species (G_SPECIES) with the following files:
     - G_SPECIES.WS228.genomic.fa.gz                - Unmasked genomic DNA
     - G_SPECIES.WS228.genomic_masked.fa.gz         - Hard-masked (repeats replaced with Ns) genomic DNA
     - G_SPECIES.WS228.genomic_softmasked.fa.gz     - Soft-masked (repeats lower-cased) genomic DNA
     - G_SPECIES.WS228.protein.fa.gz                - Current live protein set
     - G_SPECIES.WS228.cds_transcripts.fa.gz        - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
     - G_SPECIES.WS228.ncrna_transcripts.fa.gz      - Spliced cDNA sequence for non-coding RNA transcripts
     - G_SPECIES.WS228.intergenic_sequences.fa.gz   - DNA sequence between pairs of adjacent genes
     - G_SPECIES.WS228.annotations.gff[2|3].gz      - Sequence features in either GFF2 or GFF3 format
     - G_SPECIES.WS228.ests.fa.gz                   - ESTs and mRNA sequences extracted from the public databases
     - G_SPECIES.WS228.best_blastp_hits.txt.gz      - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteains
     - G_SPECIES.WS228.*pep_package.tar.gz          - latest version of the [worm|brig|bren|rema|jap|ppa]pep package (if updated since last release)
     - annotation/                    - contains additional annotations:
        - G_SPECIES.WS228.confirmed_genes.txt.gz              - DNA sequences of all genes confirmed by EST &/or cDNA
        - G_SPECIES.WS228.cDNA2orf.txt.gz                     - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
        - G_SPECIES.WS228.geneIDs.txtgz                       - list of all current gene identifiers with CGC & molecular names (when known)
        - G_SPECIES.WS228.PCR_product2gene.txt.gz             - Mappings between PCR products and overlapping Genes
        - G_SPECIES.WS228.*oligo_mapping.txt.gz               - Oligo array mapping files
        - G_SPECIES.WS228.knockout_consortium_alleles.xml.gz  - Table of Knockout Consortium alleles
        - G_SPECIES.WS228.SRA_gene_expression.tar.gz          - Tables of gene expression values computed from SRA RNASeq data
acedb DIR                -  Everything needed to generate a local copy of the The Primary database
     - database.WS228.*.tar.gz   - compressed acedb database for new release
     - models.wrm.WS228          - the latest database schema (also in above database files)
     - WS228-WS227.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 - comparative analysis files
     - compara.WS228.tar.bz2     - gene-tree and alignment GFF files
     - wormpep_clw.WS228.sql.bz2 - ClustalW protein multiple alignments
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 47455)
------------------------------------------
Molecular_info              45796 (96.5%)
Concise_description         5849 (12.3%)
Reference                   14229 (30%)
WormBase_approved_Gene_name 26336 (55.5%)
RNAi_result                 24670 (52%)
Microarray_results          23978 (50.5%)
SAGE_transcript             19180 (40.4%)


C. elegans 

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

There are 25391 CDSs, from 20484 protein-coding genes

The 25391 sequences contain  base pairs in total.

Modified entries      266
Deleted entries       105
New entries           252
Reappeared entries    5

Net change  +152


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

       	WS228       	WS227      	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:
----------------------------
 166565019 total
 a 46865690
 c 30244493
 g 30234317
 t 46807519
 - 0
 n 12413000


Caenorhabditis briggsae Genome sequence composition:
----------------------------
 108419768 total
 a 32984239
 c 19684682
 g 19693545
 t 33054090
 - 0
 n 3003212


Caenorhabditis brenneri Genome sequence composition:
----------------------------
 190421492 total
 a 52222485
 c 32837458
 g 32882838
 t 52164077
 - 0
 n 20314634




Tier II Gene counts
---------------------------------------------
pristionchus Gene count 24216 (Coding 24216)
remanei Gene count 32431 (Coding 31471)
japonica Gene count 29962 (Coding 29962)
briggsae Gene count 23050 (Coding 21962)
brenneri Gene count 32257 (Coding 30667)
---------------------------------------------




-------------------------------------------------
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   3169




-------------------------------------------------
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   5681




-------------------------------------------------
Caenorhabditis japonica Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed               176 (0.5%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed     578 (1.6%)	Some, but not all exon bases are covered by transcript evidence
Predicted             35351 (97.9%)	No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis japonica entries with WormBase-approved Gene name   4682




-------------------------------------------------
Caenorhabditis briggsae Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed                53 (0.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed     853 (3.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted             21080 (95.9%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  21682 (98.6%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis briggsae entries with WormBase-approved Gene name   5739




-------------------------------------------------
Caenorhabditis brenneri Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              1510 (4.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    5638 (18.4%)	Some, but not all exon bases are covered by transcript evidence
Predicted             23522 (76.7%)	No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis brenneri entries with WormBase-approved Gene name   3260




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             12126 (47.8%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11232 (44.2%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2033 (8.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24610 (96.9%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            25168 (99.1%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24724


C. elegans Operons Stats
---------------------------------------------
Description: These exist as closely spaced gene clusters similar to bacterial operons
---------------------------------------------
| Live Operons        1254                |
| Genes in Operons    3354                |
---------------------------------------------


GO Annotation Stats WS228
--------------------------------------

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:  294345

Genes Stats:
----------------
Genes with GO_term connections         95532  
           IEA GO_code present         89490  
       non-IEA GO_code present         6038  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   25676  
        *citace                        2426  
        *Inherited (motif & phenotype) 15087  

GO_terms Stats:
---------------
Total No. GO_terms                     30550  
GO_terms connected to Genes            3384  
GO annotations connected with IEA      1766  
GO annotations connected with non-IEA  1608  
   Breakdown  IC - 3   IDA - 435   ISS - 147 
             IEP - 10   IGI - 137   IMP - 777 
             IPI - 77  NAS - 2     ND  - 1  
             RCA - 0   TAS - 18   


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

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

Genes with Sequence and WormBase-approved Gene names
WS228 47255 (24724 elegans / 5739 briggsae / 5681 remanei / 4682 japonica / 3260 brenneri / 3169 pristionchus)


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



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

Variation_data -  Over 65,000 variations identified by the
Itai Yanai lab and published in PMID 21367940 Genome Res.
2011 Core promoter T-blocks correlate with gene expression levels in C.
elegans. Hryshkevich U, Hashimshony T, Yanai I. were added to this release. 


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


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


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


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

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


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

WS228 models v 1.2

This cycle we see 5 model changes.

#Homology type - COG - proposed by Michael

?CDS - Start_not_found <UNIQUE> int - proposed by Michael

?Transcript - u21RNA -> piRNA conversion - proposed by Gary
    Has implications for StLouis sequence database.

?Expression_cluster - proposed by Wen

?Variation - Readthrough Text #Evidence - Proposed by Kevin
             & corresponding change in the #Molecular_change hash.

More infromation and a human readable diff can be found here:

http://wiki.wormbase.org/index.php/WS228_Models.wrm

For more info mail hinxton@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 _____________

Bug Fixes

eggNOG

missing eggNOG data can be found here: ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS228/patches/eggNOG.ace