WS220

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New release of WormBase WS220, Wormpep220 and Wormrna220 Mon Oct 25 13:22:36 BST 2010


WS220 was built by gw3
-===================================================================================-
The WS220 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.WS220.gz  - DNA sequences of all genes confirmed by EST &/or cDNA
     ii) cDNA2orf.WS220.gz         - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
    iii) geneIDs.WS220.gz          - list of all current gene identifiers with CGC & molecular names (when known)
     iv) PCR_product2gene.WS220.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) wormpep220.tar.gz         - full Wormpep distribution corresponding to WS220
    vii) wormrna220.tar.gz         - latest WormRNA release containing non-coding RNA's in the genome
   viii) best_blastp_hits_species.WS220.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.WS220.*.tar.gz   - compressed acedb database for new release
     xi) models.wrm.WS220          - the latest database schema (also in above database files)
    xii) WS220-WS219.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 47360)
------------------------------------------
Molecular_info              45681 (96.5%)
Concise_description         5704 (12%)
Reference                   14129 (29.8%)
WormBase_approved_Gene_name 26069 (55%)
RNAi_result                 24623 (52%)
Microarray_results          22109 (46.7%)
SAGE_transcript             19157 (40.4%)


C. elegans 

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

There are 20405 CDS in autoace, 24842 when counting 4437 alternate splice forms.

The 24842 sequences contain 10,928,467 base pairs in total.

Modified entries      9
Deleted entries       18
New entries           34
Reappeared entries    1

Net change  +17



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

       	WS220       	WS219      	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:
----------------------------
 169822619 total
 a 41799168
 c 31168435
 g 31196239
 t 41802890
 - 0
 n 23855887


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:
----------------------------
 190426650 total
 a 52223359
 c 32838518
 g 32883836
 t 52164943
 - 0
 n 20315994




Tier II Gene counts
---------------------------------------------
pristionchus Gene count 29638 (Coding 29639)
remanei Gene count 32431 (Coding 31476)
heterorhabditis Gene count 0 (Coding 0)
japonica Gene count 27177 (Coding 25870)
briggsae Gene count 23039 (Coding 21991)
brenneri Gene count 32292 (Coding 30707)
---------------------------------------------




-------------------------------------------------
Pristionchus pacificus Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed               425 (1.4%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed    5309 (17.9%)	Some, but not all exon bases are covered by transcript evidence
Predicted             23905 (80.7%)	No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Pristionchus pacificus entries with WormBase-approved Gene name   2797




-------------------------------------------------
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   5466




-------------------------------------------------
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   4797




-------------------------------------------------
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   5504




-------------------------------------------------
Caenorhabditis brenneri Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              1517 (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             23550 (76.7%)	No transcriptional evidence at all



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis brenneri entries with WormBase-approved Gene name   3094




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             11663 (46.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11004 (44.3%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2175 (8.8%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24647 (99.2%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24647 (99.2%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24437


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 WS220
--------------------------------------

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:  266435

Genes Stats:
----------------
Genes with GO_term connections         89198  
           IEA GO_code present         83214  
       non-IEA GO_code present         5980  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   25242  
        *citace                        2187  
        *Inherited (motif & phenotype) 14528  

GO_terms Stats:
---------------
Total No. GO_terms                     30471  
GO_terms connected to Genes            3250  
GO annotations connected with IEA      1819  
GO annotations connected with non-IEA  1426  
   Breakdown  IC - 2   IDA - 351   ISS - 128 
             IEP - 9   IGI - 116   IMP - 729 
             IPI - 68  NAS - 1     ND  - 1  
             RCA - 0   TAS - 21   


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

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

Genes with Sequence and CGC name
WS220 46095 (24437 elegans / 5504 briggsae / 5466 remanei / 4797 japonica / 3094 brenneri / 2797 pristionchus)


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



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

The Caenorhabditis sp.3 gene models and assembly was synched with the
GenBank/ENA/DDBJ version, removing E.coli contaminated contigs.

There are 304 'HOT' regions from the modENCODE project.
These are regions where there does not appear to be a concentration of
transcrtption factor binding site motifs, but many transcription
factoes are found to bind to the region by ChIP-Seq experiments.

There are 7237 new ncRNA genes identified from the modENCODE project.

The Caenorhabditis species 3 (strain PS1010) genome and predicted
genes are available with the other Tier III species on the FTP site.
It the time of this database release the official Linnean name was not
publicly available and so the files for this species are named by the
abbreviation 'c_an'.

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


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


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


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

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

We expect to add 23,000 3' UTR features from the modENCODE project to release WS221.
(These are UTR spans as displayed on the UTRome project website) splicing is not accounted for in the feature.


Prposed model changes for WS221
-------------------------------

New Class


 //////////////////////////////////////////////////////////////////////////////////////////
 //
 // Transcription_factor  class This describes a type of transcription factor (and Pol II)
 // Gary W. 14/10/2010
 //
 //////////////////////////////////////////////////////////////////////////////////////////

 ?Transcription_factor	Name UNIQUE Text
 			Position_matrix  ?Position_Matrix XREF Transcription_factor #Evidence
 			Product_of ?Gene XREF Transcription_factor
 			Remark Text #Evidence
 			Binding_site ?Feature XREF Transcription_factor



Gene Class Modifications

 		       Transcription_factor ?Transcription_factor XREF Product_of

Feature Class Modifications

 	 Score Float           // this would be a log score as indicated by the analysis used in gff dump
 	 Transcription_factor UNIQUE ?Transcription_factor XREF Binding_site

Position_Matrix Class Modifications

 		  Transcription_factor  UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3


Strain Class Modifications

< 	Made_by Text
---
> 	Made_by ?Person //updated from Text

> 	Other_name ?Text #Evidence
 	Contact ?Person
          Wild_isolate // to identify wild isolates - since genotype is free text
          Isolation GPS UNIQUE Float UNIQUE Float // Latitude +/-DD.DDDDD Longitude +/-DD.DDDDD
 	 	  Place UNIQUE ?Text
          	  Landscape UNIQUE Urban_garden
 				    Wild_forest
 				    Wild_grassland
 				    Agricultural_land
 				    Oasis
 				    Rural_garden
                  Substrate UNIQUE ?Text // e.g. snail, soil, apple, rotting fruit
 	 	  Associated_organisms ?Species
 	 	  Life_stage ?Life_stage
 	 	  Log_size_of_population UNIQUE Float
	 	  Sampled_by Text // the person who found the worms
                  Isolated_by ?Person // the person who isolated the worms from the sample


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

?Strain class
Removed:Extended_genotype ?Variation

Comment: Removed this unused tag structure as data can be stored in current
         tags and the additional information/context can be resolved at the
         display level.


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 _____________