WS229

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Release Notes

New release of WormBase WS229

WS229 was built by Mary Ann Tuli
================================

The WS229 build directory includes:
species/ DIR              -  contains a sub dir for each WormBase species (G_SPECIES) with the following files:
     - G_SPECIES.WS229.genomic.fa.gz                - Unmasked genomic DNA
     - G_SPECIES.WS229.genomic_masked.fa.gz         - Hard-masked (repeats replaced with Ns) genomic DNA
     - G_SPECIES.WS229.genomic_softmasked.fa.gz     - Soft-masked (repeats lower-cased) genomic DNA
     - G_SPECIES.WS229.protein.fa.gz                - Current live protein set
     - G_SPECIES.WS229.cds_transcripts.fa.gz        - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
     - G_SPECIES.WS229.ncrna_transcripts.fa.gz      - Spliced cDNA sequence for non-coding RNA transcripts
     - G_SPECIES.WS229.intergenic_sequences.fa.gz   - DNA sequence between pairs of adjacent genes
     - G_SPECIES.WS229.annotations.gff[2|3].gz      - Sequence features in either GFF2 or GFF3 format
     - G_SPECIES.WS229.ests.fa.gz                   - ESTs and mRNA sequences extracted from the public databases
     - G_SPECIES.WS229.best_blastp_hits.txt.gz      - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteains
     - G_SPECIES.WS229.*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.WS229.confirmed_genes.txt.gz              - DNA sequences of all genes confirmed by EST &/or cDNA
        - G_SPECIES.WS229.cDNA2orf.txt.gz                     - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
        - G_SPECIES.WS229.geneIDs.txtgz                       - list of all current gene identifiers with CGC & molecular names (when known)
        - G_SPECIES.WS229.PCR_product2gene.txt.gz             - Mappings between PCR products and overlapping Genes
        - G_SPECIES.WS229.*oligo_mapping.txt.gz               - Oligo array mapping files
        - G_SPECIES.WS229.knockout_consortium_alleles.xml.gz  - Table of Knockout Consortium alleles
        - G_SPECIES.WS229.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.WS229.*.tar.gz   - compressed acedb database for new release
     - models.wrm.WS229          - the latest database schema (also in above database files)
     - WS229-WS228.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.WS229.tar.bz2     - gene-tree and alignment GFF files
     - wormpep_clw.WS229.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 47512)
------------------------------------------------------
Molecular_info              45859 (96.5%)
Concise_description         5901 (12.4%)
Reference                   14295 (30.1%)
WormBase_approved_Gene_name 26474 (55.7%)
RNAi_result                 24684 (52%)
Microarray_results          23986 (50.5%)
SAGE_transcript             19199 (40.4%)


C. elegans 

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

There are 25547 CDSs, from 20514 protein-coding genes

The 25547 sequences contain  base pairs in total.

Modified entries      115
Deleted entries       78
New entries           234
Reappeared entries    6

Net change  +162

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

       	WS229       	WS228      	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 23048 (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   3202




-------------------------------------------------
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   5741




-------------------------------------------------
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   4735




-------------------------------------------------
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   5801




-------------------------------------------------
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   3303




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             12227 (47.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11272 (44.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2048 (8.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  24534 (96.0%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            25296 (99.0%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  24866


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 WS229
--------------------------------------

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:  294649

Genes Stats:
----------------
Genes with GO_term connections         95546  
           IEA GO_code present         89484  
       non-IEA GO_code present         6058  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   25751  
        *citace                        2456  
        *Inherited (motif & phenotype) 15080  

GO_terms Stats:
---------------
Total No. GO_terms                     30571  
GO_terms connected to Genes            3438  
GO annotations connected with IEA      1786  
GO annotations connected with non-IEA  1640  
   Breakdown  IC - 4   IDA - 445   ISS - 150 
             IEP - 11   IGI - 137   IMP - 792 
             IPI - 79  NAS - 2     ND  - 1  
             RCA - 0   TAS - 18   


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

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

Genes with Sequence and WormBase-approved Gene names
WS229 47648 (24866 elegans / 5801 briggsae / 5741 remanei / 4735 japonica / 3303 brenneri / 3202 pristionchus)


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



New Data:
---------
1) DNAse1 sites

7095 Features marking DNAse1 hypersensitive sites have been added to the database.
These have a Method of "DNAseI_hypersensitive_site".

They are from the paper:
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites
Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbo G, Zhu X, Chen R
BMC Genomics 2009, 10:92
doi:10.1186/1471-2164-10-92 PMID 19243610

http://www.biomedcentral.com/1471-2164/10/92

The hypersensitive sites found fall into three categories: those cut only by 240 U/ml, only by 480 U/ml and those cut by both.

2) Ascaris suum

A draft genome including a preliminary gene set, based on "Ascaris
suum draft genome",Rex et.al,doi:10.1038/nature10553 has been added.

GFF3 and fasta files of the protein set and genome can be
downloaded from ftp.wormbase.org in addition to accessing it through
GBrowse and blast server. Ortholog C.elegans genes are also
annotated.

3) Heterorhabditis bactieriophora:

A H.bacteriophora genome based on a draft assembly from WashU St.Louis
has been added and is available as fasta and GFF3 for download and
viewable on GBrowse and blast. A gene set is expected from the
H.bacteriphora curation group for a future release.

4) Bursephelenchus xylophilus

A draft genome of B.xylophilus based on "Genomic Insights into the
Origin of Parasitism in the Emerging Plant Pathogen Bursephelenchus
xylophilus", Kikuchi et al., doi:10.1371/journal.ppat.1002219 has been
added.

It also includes a gene set provided by the authors
and is available as fasta and GFF3 file for download from ftp.wormbase.org in addition 
to accessing it through GBrowse and blast.


Other Changes:
--------------
1) Genome Sequence error sites

A set of errors in the reference sequence have been identified by comparison of the N2 genome to the sister strain LSJ2 (which diverged from 
N2 before N2 was split up into lab specific strains):

Nature. 2011 Aug 17;477(7364):321-5. doi: 10.1038/nature10378.
Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes.
McGrath PT, Xu Y, Ailion M, Garrison JL, Butcher RA, Bargmann CI.

This has resulted in 882 Features with the Method "Genome_sequence_error"  being made to mark the positions of the insertion or deletion errors.
The reference sequence has not yet been changed as a consequence because changes to the reference sequence make difficulties for people who 
require a stable genome sequence coordinate system.

There are 39 CDS models that will be changed as a consequence of these sequence errors and there are 15 Pseudogenes that will be 
re-examined because of these errors.

2) GI numbers have been updated to use the Nov 2011 GI protein IDs.


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

1) ?Strain - new tags: 
          Sample_history Text
          Date_first_frozen UNIQUE DateType


2) ?Gene/?CDS/?Pseudogene/?Transcript - new tag:

              RNASeq_FPKM  ?Life_stage  Float  #Evidence

Notes: FPKM is the cufflinks measure of RNASeq transcript abundance - "Fragments Per Kilobase of exon per Million fragments mapped". 
Is like RPKM, but makes a correction for when using paired-reads.



Modifications:

3) ?Sequence 

                       Checksum MD5 Text     //checksums should only be created for an upper-cased sequence.
                                CRC64 Text   //checksums should only be created for an upper-cased sequence.

becomes:

                       Checksum MD5 UNIQUE Text     //checksums should only be created for an upper-cased sequence.
                                CRC64 UNIQUE Text   //checksums should only be created for an upper-cased sequence.

4) ?Transcript - Cosmetic change to allow ACeDB code to dump the data stored in this tag correctly. 

                       Brief_identification UNIQUE Text                           // [020306 kj]

becomes:

                       Brief_identification UNIQUE ?Text


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 _____________

Bug Fixes

DB_remarks

Missing DB remarks data can be found here ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS229/patches/misc_DB_remark.ace