WS224

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New release of WormBase WS224, Wormpep224 and Wormrna224 Fri Mar  4 14:58:13 GMT 2011


WS224 was built by Mary Ann Tuli
-===================================================================================-
The WS224 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.WS224.gz  - DNA sequences of all genes confirmed by EST &/or cDNA
     ii) cDNA2orf.WS224.gz         - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
    iii) geneIDs.WS224.gz          - list of all current gene identifiers with CGC & molecular names (when known)
     iv) PCR_product2gene.WS224.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) wormpep224.tar.gz         - full Wormpep distribution corresponding to WS224
    vii) wormrna224.tar.gz         - latest WormRNA release containing non-coding RNA's in the genome
   viii) best_blastp_hits_species.WS224.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.WS224.*.tar.gz   - compressed acedb database for new release
     xi) models.wrm.WS224          - the latest database schema (also in above database files)
    xii) WS224-WS223.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 47387)
------------------------------------------
Molecular_info              45719 (96.5%)
Concise_description         5736 (12.1%)
Reference                   14138 (29.8%)
WormBase_approved_Gene_name 26116 (55.1%)
RNAi_result                 24628 (52%)
Microarray_results          22118 (46.7%)
SAGE_transcript             19125 (40.4%)


C. elegans 

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

There are 20430 CDS in autoace, 25010 when counting 4580 alternate splice forms.

The 25010 sequences contain 10,980,936 base pairs in total.

Modified entries      48
Deleted entries       46
New entries           97
Reappeared entries    2

Net change  +53
The differnce between the total CDS's of this (25010) and the last build (24959) does not equal the net change 53
Please investigate! ! 


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

       	WS224       	WS223      	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:
----------------------------
 108419768 total
 a 32984239
 c 19684682
 g 19693545
 t 33054090
 - 0
 n 3003212


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 23052 (Coding 21963)
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   3078




-------------------------------------------------
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   5499




-------------------------------------------------
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   4834




-------------------------------------------------
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     854 (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  21683 (98.6%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis briggsae entries with WormBase-approved Gene name   5544




-------------------------------------------------
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   3123




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             11801 (47.2%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11033 (44.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2176 (8.7%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24707 (98.8%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            24822 (99.2%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24493


C. elegans Operons Stats
---------------------------------------------
Description: These exist as closely spaced gene clusters similar to bacterial operons
---------------------------------------------
| Live Operons        1288                |
| Genes in Operons    3341                |
---------------------------------------------


GO Annotation Stats WS224
--------------------------------------

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:  252001

Genes Stats:
----------------
Genes with GO_term connections         86456  
           IEA GO_code present         80572  
       non-IEA GO_code present         5880  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   24507  
        *citace                        2267  
        *Inherited (motif & phenotype) 15090  

GO_terms Stats:
---------------
Total No. GO_terms                     30483  
GO_terms connected to Genes            3336  
GO annotations connected with IEA      1856  
GO annotations connected with non-IEA  1474  
   Breakdown  IC - 3   IDA - 375   ISS - 136 
             IEP - 9   IGI - 120   IMP - 736 
             IPI - 72  NAS - 1     ND  - 1  
             RCA - 0   TAS - 20   


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

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

Genes with Sequence and CGC name
WS224 46571 (24493 elegans / 5544 briggsae / 5499 remanei / 4834 japonica / 3123 brenneri / 3078 pristionchus)


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



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


Genome sequence updates:
-----------------------
Caenorhabditis briggsae

This build includes a new genome assembly (cb4) for C. briggsae (Haag Laboratory, 
Department of Biology, University of Maryland). Briefly, 167 AF16/HK104 advanced-intercross 
recombinant inbred lines were successfully genotyped at 1,032 single nucleotide polymorphism 
(SNP) markers. The resulting data were used to estimate high-density genetic maps. Sequences 
were assembled by combining the physical (cb25 assembly; [Stein et al. 2003 PMID:14624247]) 
and genetic positions of the SNPs to inform the process of ordering and orienting the cb25 
supercontigs into chromosome assemblies. Detailed methods will be published subsequently 
[Ross JA et al, 2011 PLOS Genetics, in review]. 

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


Known Problems:
---------------
1. An ACeDB patch for containing the missing ortology and paralogy data
can be found at:
ftp://ftp.sanger.ac.uk/pub2/wormbase/WS224/acedb/patch/compara.ace.bz2

2. Due to technical reasons Heterorhabditis bacteriophora ESTs were
excluded in the BLAT alignments of C.briggsae and C.elegans. We
intend to add them back into the next frozen release WS225.


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

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

WS225 will include the draft Trichinella spiralis genome of Mitreva, et.al
Connections to orthologeaous Trichinella spiralis proteins will be
included for all genes, as well as an annotated Genome Browser.


Model Changes:
------------------------------------
This cycle sees the introduction of the WBProcess class model.


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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