WS227
From WormBaseWiki
Jump to navigationJump to searchRelease Letter
New release of WormBase WS227
WS227 was built by Michael Paulini
-===================================================================================-
The WS227 build directory includes:
species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
- G_SPECIES.WS227.genomic.fa.gz - Unmasked genomic DNA
- G_SPECIES.WS227.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
- G_SPECIES.WS227.genomic_softmasked.fa.gz - Soft-masked (repeats lower-cased) genomic DNA
- G_SPECIES.WS227.protein.fa.gz - Current live protein set
- G_SPECIES.WS227.cds_transcripts.fa.gz - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
- G_SPECIES.WS227.ncrna_transcripts.fa.gz - Spliced cDNA sequence for non-coding RNA transcripts
- G_SPECIES.WS227.intergenic_sequences.fa.gz - DNA sequence between pairs of adjacent genes
- G_SPECIES.WS227.annotations.gff[2|3].gz - Sequence features in either GFF2 or GFF3 format
- G_SPECIES.WS227.ests.fa.gz - ESTs and mRNA sequences extracted from the public databases
- G_SPECIES.WS227.best_blastp_hits.txt.gz - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteains
- G_SPECIES.WS227.*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.WS227.confirmed_genes.txt.gz - DNA sequences of all genes confirmed by EST &/or cDNA
- G_SPECIES.WS227.cDNA2orf.txt.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
- G_SPECIES.WS227.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known)
- G_SPECIES.WS227.PCR_product2gene.txt.gz - Mappings between PCR products and overlapping Genes
- G_SPECIES.WS227.*oligo_mapping.txt.gz - Oligo array mapping files
- G_SPECIES.WS227.knockout_consortium_alleles.xml.gz - Table of Knockout Consortium alleles
- G_SPECIES.WS227.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.WS227.*.tar.gz - compressed acedb database for new release
- models.wrm.WS227 - the latest database schema (also in above database files)
- WS227-WS226.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.WS227.tar.bz2 - gene-tree and alignment GFF files
- wormpep_clw.WS227.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 47408)
------------------------------------------
Molecular_info 45748 (96.5%)
Concise_description 5808 (12.3%)
Reference 14208 (30%)
WormBase_approved_Gene_name 26299 (55.5%)
RNAi_result 24641 (52%)
Microarray_results 23973 (50.6%)
SAGE_transcript 19163 (40.4%)
C. elegans
Wormpep data set:
----------------------------
There are 25244 CDSs, from 20470 protein-coding genes
The 25244 sequences contain 11,068,632 base pairs in total.
Modified entries 58
Deleted entries 23
New entries 96
Reappeared entries 1
Net change +74
C. elegans Genome sequence composition:
----------------------------
WS227 WS226 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 23050 (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 3153
-------------------------------------------------
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 5655
-------------------------------------------------
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 4652
-------------------------------------------------
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 5705
-------------------------------------------------
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 3236
-------------------------------------------------
Caenorhabditis elegans Protein Stats:
-------------------------------------------------
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed 12052 (47.7%) Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed 11172 (44.3%) Some, but not all exon bases are covered by transcript evidence
Predicted 2020 (8.0%) No transcriptional evidence at all
Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions 24444 (96.8%)
Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id 24594 (97.4%)
Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 24684
C. elegans Operons Stats
---------------------------------------------
Description: These exist as closely spaced gene clusters similar to bacterial operons
---------------------------------------------
| Live Operons 1253 |
| Genes in Operons 3348 |
---------------------------------------------
GO Annotation Stats WS227
--------------------------------------
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: 293205
Genes Stats:
----------------
Genes with GO_term connections 95463
IEA GO_code present 89531
non-IEA GO_code present 5928
Source of the mapping data
Source: *RNAi (GFF mapping overlaps) 25387
*citace 2249
*Inherited (motif & phenotype) 15069
GO_terms Stats:
---------------
Total No. GO_terms 30542
GO_terms connected to Genes 3321
GO annotations connected with IEA 1766
GO annotations connected with non-IEA 1544
Breakdown IC - 3 IDA - 419 ISS - 141
IEP - 10 IGI - 132 IMP - 740
IPI - 74 NAS - 2 ND - 1
RCA - 0 TAS - 21
-===================================================================================-
Useful Stats:
---------
Genes with Sequence and WormBase-approved Gene names
WS227 47085 (24684 elegans / 5705 briggsae / 5655 remanei / 4652 japonica / 3236 brenneri / 3153 pristionchus)
-===================================================================================-
New Data:
---------
* Introns confirmed by RNASeq based on C.elegans and C.briggsae SRA data (as GFF tracks and ACeDB features)
* Caenorhabditis species 11 gene models have been updated with Augustus models based on RNASeq from Erich Schwartz
* imported H.sapiens ortholog predictions from TreeFam
* imported orthologs/paralogs from PantherDB
* added eggNOG homology_groups from Peer Bork's lab
* C.japonica gene models based on ESTs/cDNAs/RNASeq added (based on Erich Schwartz RNASeq predictions)
Genome sequence updates:
-----------------------
* removed contaminated C.brenneri contigs based on feedback of INSDC (now in sync with INSDC)
* C.japonica assembly update to WashU version 7.0.1
New Fixes:
----------
Known Problems:
---------------
* It has been discovered that C. species 7 & 9 have contamination in their assemblies. Please proceed with caution if using this data.
Other Changes:
--------------
* removed outdated Inparanoid homology_groups, as they have been superceded by Inparanoid orthologs
* removed outdated KOG homology_groups, as they have been superceded by eggNOG
* multiple genome alignments changed to 11 species (C.elegans, C.brenneri, C.sp11, C.remanei,C.briggsae,C.japonica,C.angaria,P.pacificus,M.hapla,B.malayi and T.spiralis)
Proposed Changes / Forthcoming Data:
-------------------------------------
Model Changes:
------------------------------------
* changes to the Transgene model
* changes to the Gene model to allow curation for human disease relevance
* new Rearrangment type Introgression
* Sequence checksums
* Splice_confirmation hash changes to allow for RNASeq and Mass-pec data
* Sequence collections to represent assemblies
* changes to the Homology_type hash to allow more eggNOG types
* changes to the Feature class to allow quantification/scoring
* cleanups in the Movie and Gene class
* addition of an Affiliation to the Person class
* addition of an Fax number to the Address hash
* addition of Rearrangements to the Molecule class
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 _____________
Optional Patches
eggNOG protein-gene connections
All proteins of the eggNOG database have connections to all WormBase genes of their cluster in WS227. As that drowns out the other member databases (InParanoid/TreeFam/Panther/...), there is a patch to remove these connection for better visualisation. ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS227/patches/patch1_eggNOG.ace.gz
