WS232

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Release notes for WS232

New release of WormBase WS232

WS232 was built by Michael Paulini [michael.paulini@wormbase.org]
-===================================================================================-
The WS232 build directory includes:
species/ DIR              -  contains a sub dir for each WormBase species (G_SPECIES) with the following files:
     - G_SPECIES.WS232.genomic.fa.gz                - Unmasked genomic DNA
     - G_SPECIES.WS232.genomic_masked.fa.gz         - Hard-masked (repeats replaced with Ns) genomic DNA
     - G_SPECIES.WS232.genomic_softmasked.fa.gz     - Soft-masked (repeats lower-cased) genomic DNA
     - G_SPECIES.WS232.protein.fa.gz                - Current live protein set
     - G_SPECIES.WS232.cds_transcripts.fa.gz        - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
     - G_SPECIES.WS232.ncrna_transcripts.fa.gz      - Spliced cDNA sequence for non-coding RNA transcripts
     - G_SPECIES.WS232.intergenic_sequences.fa.gz   - DNA sequence between pairs of adjacent genes
     - G_SPECIES.WS232.annotations.gff[2|3].gz      - Sequence features in either GFF2 or GFF3 format
     - G_SPECIES.WS232.ests.fa.gz                   - ESTs and mRNA sequences extracted from the public databases
     - G_SPECIES.WS232.best_blastp_hits.txt.gz      - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteins
     - G_SPECIES.WS232.*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.WS232.confirmed_genes.txt.gz              - DNA sequences of all genes confirmed by EST &/or cDNA
        - G_SPECIES.WS232.cDNA2orf.txt.gz                     - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
        - G_SPECIES.WS232.geneIDs.txtgz                       - list of all current gene identifiers with CGC & molecular names (when known)
        - G_SPECIES.WS232.PCR_product2gene.txt.gz             - Mappings between PCR products and overlapping Genes
        - G_SPECIES.WS232.*oligo_mapping.txt.gz               - Oligo array mapping files
        - G_SPECIES.WS232.knockout_consortium_alleles.xml.gz  - Table of Knockout Consortium alleles
        - G_SPECIES.WS232.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.WS232.*.tar.gz   - compressed acedb database for new release
     - models.wrm.WS232          - the latest database schema (also in above database files)
     - WS232-WS231.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.WS232.tar.bz2     - gene-tree and alignment GFF files
     - wormpep_clw.WS232.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 47556)
------------------------------------------
Molecular_info              45911 (96.5%)
Concise_description         5971 (12.6%)
Reference                   17204 (36.2%)
WormBase_approved_Gene_name 26801 (56.4%)
RNAi_result                 24690 (51.9%)
Microarray_results          23990 (50.4%)
SAGE_transcript             19220 (40.4%)


C. elegans 

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

There are 25987 CDSs, from 20553 protein-coding genes

The 25987 sequences contain 34451067 base pairs in total.

Modified entries      77
Deleted entries       58
New entries           197
Reappeared entries    7

Net change  +146
The difference (139) between the total CDS's of this (25987) and the last build (25848) does not equal the net change 146
Please investigate! ! 


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

       	WS232       	WS231      	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
 - 62600
 n 2940612


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 32414 (Coding 31445)
japonica Gene count 29962 (Coding 29962)
briggsae Gene count 23027 (Coding 21936)
brenneri Gene count 32331 (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   3248




-------------------------------------------------
Caenorhabditis remanei Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed               961 (3.1%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    5658 (18.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted             24831 (79.0%)	No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis remanei entries with WormBase-approved Gene name   5982




-------------------------------------------------
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   4945




-------------------------------------------------
Caenorhabditis briggsae Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed                54 (0.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed     859 (3.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted             21048 (95.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  21662 (98.6%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis briggsae entries with WormBase-approved Gene name   6064




-------------------------------------------------
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   3484




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             12440 (47.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11472 (44.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2075 (8.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  25814 (99.3%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            25975 (100.0%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  25201


C. elegans Operons Stats
---------------------------------------------
Description: These exist as closely spaced gene clusters similar to bacterial operons
---------------------------------------------
| Live Operons        1390                |
| Genes in Operons    3634                |
---------------------------------------------


GO Annotation Stats WS232
--------------------------------------

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:  290838

Genes Stats:
----------------
Genes with GO_term connections         96609  
           IEA GO_code present         91223  
       non-IEA GO_code present         5382  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   20107  
        *citace                        2560  
        *Inherited (motif & phenotype) 15076  

GO_terms Stats:
---------------
Total No. GO_terms                     30606  
GO_terms connected to Genes            3572  
GO annotations connected with IEA      1833  
GO annotations connected with non-IEA  1722  
   Breakdown  IC - 6   IDA - 501   ISS - 148 
             IEP - 11   IGI - 148   IMP - 803 
             IPI - 84  NAS - 1     ND  - 1  
             RCA - 0   TAS - 18   


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

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

Genes with Sequence and WormBase-approved Gene names
WS232 48924 (25201 elegans / 6064 briggsae / 5982 remanei / 4945 japonica / 3484 brenneri / 3248 pristionchus)


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



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

New Transcriptionally Active Region Features

The Tiling Array data specifying Transcriptionallly Active Regions (TARs) from David Miller's lab:
http://intermine.modencode.org/query/experiment.do?experiment=Identification+of+tissue+and+stage-specific+transcribed+sequences+with+expression+profile+maps
has been added to the database as Feature_data objects with a GFF source of 'TranscriptionallyActiveRegion'.


Genome sequence updates:
-----------------------
C.angaria update

The C.angaria assembly has been updated to the latest genome draft available from the Schwarz lab at CalTech. 
It also includes a new set of gene predictions provided by CalTech, and can be downloaded from 
ftp://ftp.wormbase.org/pub/wormbase/releases/WS232/species/c_angaria

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


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


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

C.elegans genetic map frozen

The genetic map of C. elegans has changed very little in the past
three years in terms of recombinational map distances and marker gene
locations. It is therefore being frozen, from WS232 onward. In future,
new genetic loci, deficiencies and duplications will continue
to be added to the genetic map, but these will simply be interpolated
into the existing map.



Renaming of naturally occurring variation data

From WS232 on, all naturally occurring variation data objects will be identified
by their WBVariationID. Two datasets are currently named in accordance
with this policy in WS232:

1) PMID 21849976 McGrath PT et al. (2011) Nature "Parallel evolution of
domesticated Caenorhabditis species targets pheromone ...."

2) Cutter/Stein - four distinct C.elegans strains vs. N2.


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

Renaming of all naturally occurring variations already held in
WormBase will be complete in WS233.



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

1.) ?Interaction and #Interactor_info

#Interactor_info
Remove:
Antibody
Remark

Rename:
Antibody_info -> Antibody


?Interaction
Add:
Antibody_remark ?Text


More infromation and a human readable diff can be found here:
http://wiki.wormbase.org/index.php/WS232_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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