WS231

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Release notes for WS231

New release of WormBase WS231

WS231 was built by gw3
-===================================================================================-
The WS231 build directory includes:
species/ DIR              -  contains a sub dir for each WormBase species (G_SPECIES) with the following files:
     - G_SPECIES.WS231.genomic.fa.gz                - Unmasked genomic DNA
     - G_SPECIES.WS231.genomic_masked.fa.gz         - Hard-masked (repeats replaced with Ns) genomic DNA
     - G_SPECIES.WS231.genomic_softmasked.fa.gz     - Soft-masked (repeats lower-cased) genomic DNA
     - G_SPECIES.WS231.protein.fa.gz                - Current live protein set
     - G_SPECIES.WS231.cds_transcripts.fa.gz        - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
     - G_SPECIES.WS231.ncrna_transcripts.fa.gz      - Spliced cDNA sequence for non-coding RNA transcripts
     - G_SPECIES.WS231.intergenic_sequences.fa.gz   - DNA sequence between pairs of adjacent genes
     - G_SPECIES.WS231.annotations.gff[2|3].gz      - Sequence features in either GFF2 or GFF3 format
     - G_SPECIES.WS231.ests.fa.gz                   - ESTs and mRNA sequences extracted from the public databases
     - G_SPECIES.WS231.best_blastp_hits.txt.gz      - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteins
     - G_SPECIES.WS231.*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.WS231.confirmed_genes.txt.gz              - DNA sequences of all genes confirmed by EST &/or cDNA
        - G_SPECIES.WS231.cDNA2orf.txt.gz                     - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
        - G_SPECIES.WS231.geneIDs.txtgz                       - list of all current gene identifiers with CGC & molecular names (when known)
        - G_SPECIES.WS231.PCR_product2gene.txt.gz             - Mappings between PCR products and overlapping Genes
        - G_SPECIES.WS231.*oligo_mapping.txt.gz               - Oligo array mapping files
        - G_SPECIES.WS231.knockout_consortium_alleles.xml.gz  - Table of Knockout Consortium alleles
        - G_SPECIES.WS231.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.WS231.*.tar.gz   - compressed acedb database for new release
     - models.wrm.WS231          - the latest database schema (also in above database files)
     - WS231-WS230.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.WS231.tar.bz2     - gene-tree and alignment GFF files
     - wormpep_clw.WS231.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 47528)
------------------------------------------
Molecular_info              45878 (96.5%)
Concise_description         5952 (12.5%)
Reference                   14424 (30.3%)
WormBase_approved_Gene_name 26726 (56.2%)
RNAi_result                 24687 (51.9%)
Microarray_results          23985 (50.5%)
SAGE_transcript             19204 (40.4%)


C. elegans 

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

There are 25848 CDSs, from 20513 protein-coding genes

The 25848 sequences contain 34300239 base pairs in total.

Modified entries      167
Deleted entries       108
New entries           322
Reappeared entries    3

Net change  +217


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

       	WS231       	WS230      	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 32431 (Coding 31471)
japonica Gene count 29962 (Coding 29962)
briggsae Gene count 23027 (Coding 21936)
brenneri Gene count 32284 (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   3226




-------------------------------------------------
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   5928




-------------------------------------------------
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   4899




-------------------------------------------------
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   6001




-------------------------------------------------
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   3443




-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed             12388 (47.9%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   11403 (44.1%)	Some, but not all exon bases are covered by transcript evidence
Predicted              2057 (8.0%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  25577 (99.0%)

Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            25836 (100.0%)

Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  25124


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 WS231
--------------------------------------

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:  295368

Genes Stats:
----------------
Genes with GO_term connections         95547  
           IEA GO_code present         89448  
       non-IEA GO_code present         6095  

Source of the mapping data             
Source: *RNAi (GFF mapping overlaps)   26056  
        *citace                        2541  
        *Inherited (motif & phenotype) 15097  

GO_terms Stats:
---------------
Total No. GO_terms                     30601  
GO_terms connected to Genes            3563  
GO annotations connected with IEA      1817  
GO annotations connected with non-IEA  1730  
   Breakdown  IC - 6   IDA - 498   ISS - 152 
             IEP - 11   IGI - 146   IMP - 811 
             IPI - 85  NAS - 1     ND  - 1  
             RCA - 0   TAS - 18   


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

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

Genes with Sequence and WormBase-approved Gene names
WS231 48621 (25124 elegans / 6001 briggsae / 5928 remanei / 4899 japonica / 3443 brenneri / 3226 pristionchus)


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



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

eggNOG
======

eggNOG has been updated to Version 3
http://eggnog.embl.de/version_3.0/

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
Groups) is a database of orthologous groups of genes. The orthologous
groups are annotated with functional description lines (derived by
identifying a common denominator for the genes based on their various
annotations), with functional categories (i.e derived from the
original COG/KOG categories).


Data from the Andy Fire lab
===========================

The Lamm et al. (2011) paper describes three techniques for doing
RNASeq reads.  As part of their work they find TSL sites and polyA
sites.

They also find reads that are part of the polysome fraction of RNAs -
these are regions that are being actively translated as well as just
transcribed.

The data was downloaded from GEO:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22410


Lamm AT, Stadler MR, Zhang H, Gent JI et al. "Multimodal RNA-seq using
single-strand, double-strand, and CircLigase-based capture yields a
refined and extended description of the C. elegans
transcriptome." Genome Res 2011 Feb;21(2):265-75. PMID: 21177965

No of new SL1 features: 504
No of new SL2 features: 36
No of new polyA_site features: 10936
There is a new 'polysome' set of FeatureData objects.


modENCODE Aggregate CDS structures
==================================

We have updated the modENCODE Aggregate CDS structures to version "AG1110.v1201"

Heterorhabditis bacteriophora
=============================

The WormBase H.bacteriophora data (genome assembly and gene structure
annotation) has been updated to the latest (February 2012) INSDC
submission of the H.bacteriophora annotation project.


BLAST databases
===============

The following blast databases were updated to the latest versions for
this Build:

gadfly
trembl
swissprot
wormpep


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


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


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


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

We are changing the GFF source for the nGASP prediction sets for WS231
(to clearly disambiguate them from other runs of the same programs,
which we also dump). The old->new source map is:

AUGUSTUS => nGASP_AUGUSTUS
FGENESH  => nGASP_FGENESH
mGENE => nGASP_mGENE
nGASP => nGASP_jigsaw


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


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

WS231 models

This cycle we see 6 model changes.

i) Unified Interaction model - major re-working of the Interaction class

http://wiki.wormbase.org/index.php/WormBase_Model:Interaction

ii) Legacy data incorporation (Variation Phenotype_info)

iii) New Homology type nemNOG

iv) Re-homing of Rescued_by_Transgene from Variation -> Phenotype_info

v) Removal of Accession_number XREF from the Homology_group

vi) ?Transposon, Corresponding_CDS and Corresponding_Pseudogene -

More information and a human readable diff can be found here:
http://wiki.wormbase.org/index.php/WS231_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.

____________  END _____________