WS284
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New release of WormBase WS284
WS284 was built by Stavros Diamantakis
-==============================================================================-
-========= FTP site structure =================================================-
-==============================================================================-
The WS284 build directory includes:
species/ DIR - contains a sub dir for each WormBase species (G_SPECIES)
species/G_SPECIES DIR - contains a sub dir for each NCBI genome sequencing BioProject (BIOPROJECT) for the species, with the following files:
- G_SPECIES.BIOPROJECT.WS284.genomic.fa.gz - Unmasked genomic DNA
- G_SPECIES.BIOPROJECT.WS284.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
- G_SPECIES.BIOPROJECT.WS284.genomic_softmasked.fa.gz - Soft-masked (repeats lower-cased) genomic DNA
- G_SPECIES.BIOPROJECT.WS284.protein.fa.gz - Current live protein set
- G_SPECIES.BIOPROJECT.WS284.CDS_transcripts.fa.gz - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
- G_SPECIES.BIOPROJECT.WS284.mRNA_transcripts.fa.gz - Spliced cDNA sequence for the full-length (including UTRs) mRNA for transcripts
- G_SPECIES.BIOPROJECT.WS284.ncrna_transcripts.fa.gz - Spliced cDNA sequence for non-coding RNA transcripts
- G_SPECIES.BIOPROJECT.WS284.pseudogenic_transcripts.fa.gz - Spliced cDNA sequence for pseudogenic transcripts
- G_SPECIES.BIOPROJECT.WS284.transposon_transcripts.fa.gz - Spliced cDNA sequence for mRNAs and pseudogenes located in Transposons
- G_SPECIES.BIOPROJECT.WS284.transposons.fa.gz - DNA sequence of curated and predicted Transposons
- G_SPECIES.BIOPROJECT.WS284.transposon_cds.pep.gz - Protein sequence of curated CDSs associated with Transposons
- G_SPECIES.BIOPROJECT.WS284.intergenic_sequences.fa.gz - DNA sequence between pairs of adjacent genes
- G_SPECIES.BIOPROJECT.WS284.annotations.gff[2|3].gz - Sequence features in either GFF2 or GFF3 format
- G_SPECIES.BIOPROJECT.WS284.protein_annotation.gff3.gz - Sequence features in proteins in GFF3 format
- G_SPECIES.BIOPROJECT.WS284.canonical_geneset.gtf.gz - Genes, transcripts and CDSs in GTF (GFF2) format
- G_SPECIES.BIOPROJECT.WS284.ests.fa.gz - ESTs and mRNA sequences extracted from the public databases
- G_SPECIES.BIOPROJECT.WS284.best_blastp_hits.txt.gz - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteins
- G_SPECIES.BIOPROJECT.WS284.*pep_package.tar.gz - latest version of the [worm|brig|bren|rema|jap|ppa|brug]pep package (if updated since last release)
- annotation/ - contains additional annotations:
- G_SPECIES.BIOPROJECT.WS284.confirmed_genes.txt.gz - DNA sequences of all genes confirmed by EST &/or cDNA
- G_SPECIES.BIOPROJECT.WS284.cDNA2orf.txt.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
- G_SPECIES.BIOPROJECT.WS284.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known)
- G_SPECIES.BIOPROJECT.WS284.PCR_product2gene.txt.gz - Mappings between PCR products and overlapping Genes
- G_SPECIES.BIOPROJECT.WS284.*oligo_mapping.txt.gz - Oligo array mapping files
- G_SPECIES.BIOPROJECT.WS284.knockout_consortium_alleles.xml.gz - Table of Knockout Consortium alleles
- G_SPECIES.BIOPROJECT.WS284.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
- G_SPECIES.BIOPROJECT.WS284.TSS.wig.tar.gz - Wiggle plot files of Transcription Start Sites from the papers WBPaper00042246, WBPaper00042529, WBPaper00042354
- G_SPECIES.BIOPROJECT.WS284.repeats.fa..gz - Latest version of the repeat library for the genome, suitable for use with RepeatMasker
acedb DIR - Everything needed to generate a local copy of the The Primary database
- database.WS284.*.tar.gz - compressed acedb database for new release
- models.wrm.WS284 - the latest database schema (also in above database files)
- WS284-WS283.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)
MULTI_SPECIES DIR - miscellaneous files with data for multiple species
- wormpep_clw.WS284.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/about/release_schedule
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-=========== C. elegans data summary =================================================-
-=====================================================================================-
Genome version
The version of the C. elegans reference genome included with this release is:
Version Name: WBcel235
INSDC accession: GCA_000002985.3
UNSC name: ce11
This version has been present in WormBase since release WS235
C. elegans gene data (49176 genes in total)
Protein-coding (19981 genes):
Curated description 5098 (25.5%)
Automated description 19842 (99.3%)
Human disease association 3499 (17.5%)
Approved Gene name 10613 (53.1%)
Reference 11537 (57.7%)
RNAi results 18338 (91.8%)
Microarray results 19774 (99.0%)
Expression patterns 19414 (97.2%)
Variations 19977 (100.0%)
Interaction data 16116 (80.7%)
Non-coding RNA and pseudogene (27670 genes):
Curated description 219 (0.8%)
Automated description 7162 (25.9%)
Human disease association 29 (0.1%)
Approved Gene name 16526 (59.7%)
Reference 5901 (21.3%)
RNAi results 861 (3.1%)
Microarray results 2268 (8.2%)
Expression patterns 896 (3.2%)
Variations 27634 (99.9%)
Interaction data 943 (3.4%)
Uncloned (1525 genes):
Curated description 779 (51.1%)
Automated description 116 (7.6%)
Human disease association 10 (0.7%)
Approved Gene name 1525 (100.0%)
Reference 1122 (73.6%)
RNAi results 0 (0.0%)
Microarray results 0 (0.0%)
Expression patterns 18 (1.2%)
Variations 1185 (77.7%)
Interaction data 140 (9.2%)
Wormpep data set:
There are 28556 CDSs, from 19978 protein-coding loci
The 28556 sequences contain 40753491 base pairs in total.
Modified entries 12
Deleted entries 15
New entries 25
Reappeared entries 0
Net change +10
C. elegans Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 23524 (82.4%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 4045 (14.2%) Some, but not all exon bases are covered by transcript evidence
Predicted 987 (3.5%) No coverage by mRNA/EST/RNASeq evidence
C. elegans Operons Stats
Live Operons 1385
Genes in Operons 3688
C. elegans GO annotation status
GO_codes - used for assigning evidence
IBA Inferred by Biological aspect of Ancestor
IC Inferred by Curator
IDA Inferred from Direct Assay
IEA Inferred from Electronic Annotation
IEP Inferred from Expression Pattern
IGI Inferred from Genetic Interaction
IKR Inferred from Key Residues
IMP Inferred from Mutant Phenotype
IPI Inferred from Physical Interaction
IRD Inferred from Rapid Divergence
ISM Inferred from Sequence Model
ISO Inferred from Sequence Orthology
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
Number of gene<->GO_term associations 133555
Breakdown by annotation provider:
WormBase 18751
UniProt 56189
GO_Central 29928
InterPro 21495
GOC 2632
IntAct 2388
RHEA 1993
SynGO 36
CACAO 36
ParkinsonsUK-UCL 30
MGI 29
BHF-UCL 23
HGNC-UCL 14
CAFA 7
ARUK-UCL 2
HGNC 1
FlyBase 1
Breakdown by evidence code:
IEA 73131
Interpro2GO 21496
Other 51635
non-IEA 60424
EXP 1
HDA 386
HEP 319
IBA 29915
IC 116
IDA 7790
IEP 170
IGI 4672
IKR 5
IMP 10169
IPI 4232
ISM 9
ISO 1
ISS 1867
NAS 180
ND 406
RCA 13
TAS 173
Genes Stats:
Genes with GO_term connections 14379
Non-IEA-only annotation 1250
IEA-only annotation 5024
Both IEA and non-IEA annotations 8105
GO_term Stats:
Distinct GO_terms connected to Genes 7046
Associated by non-IEA only 3870
Associated by IEA only 803
Associated by both IEA and non-IEA 2373
-=============================================================================-
-=========== Other core species data summary =================================-
-=============================================================================-
Assembly versions
Brugia malayi B_malayi-4.0 (project PRJNA10729, current since WS252)
Caenorhabditis brenneri C_brenneri-6.0.1b (project PRJNA20035, current since WS227)
Caenorhabditis briggsae CB4 (project PRJNA10731, current since WS254)
Caenorhabditis japonica C_japonica-7.0.1 (project PRJNA12591, current since WS227)
Caenorhabditis remanei C_remanei-15.0.1 (project PRJNA53967, current since WS185)
Onchocerca volvulus O_volvulus_Cameroon_v3 (project PRJEB513, current since WS241)
Pristionchus pacificus P_pacificus-El_Paco (project PRJNA12644, current since WS263)
Strongyloides ratti S_ratti_ED321_v5_0_4 (project PRJEB125, current since WS247)
Trichuris muris T_muris-TMUE3.1 (project PRJEB126, current since WS264)
Approved gene symbols
Brugia malayi 4163
Caenorhabditis brenneri 8528
Caenorhabditis briggsae 8002
Caenorhabditis japonica 6824
Caenorhabditis remanei 8492
Onchocerca volvulus 3213
Pristionchus pacificus 4341
Strongyloides ratti 109
Trichuris muris 0
Gene counts
Brugia malayi 11687 (10936 coding)
Caenorhabditis brenneri 33291 (30705 coding)
Caenorhabditis briggsae 23202 (21024 coding)
Caenorhabditis japonica 32410 (29935 coding)
Caenorhabditis remanei 59263 (57627 coding)
Onchocerca volvulus 12605 (12109 coding)
Pristionchus pacificus 26343 (26342 coding)
Strongyloides ratti 12973 (12464 coding)
Trichuris muris 15754 (14995 coding)
Brugia malayi Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 8148 (53.6%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 5704 (37.5%) Some, but not all exon bases are covered by transcript evidence
Predicted 1352 (8.9%) No coverage by mRNA/EST/RNASeq evidence
Caenorhabditis brenneri Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 1593 (5.2%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 5706 (18.6%) Some, but not all exon bases are covered by transcript evidence
Predicted 23426 (76.2%) No coverage by mRNA/EST/RNASeq evidence
Caenorhabditis briggsae Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 16526 (68.8%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 4559 (19.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 2923 (12.2%) No coverage by mRNA/EST/RNASeq evidence
Caenorhabditis japonica Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 9390 (26.1%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 12173 (33.8%) Some, but not all exon bases are covered by transcript evidence
Predicted 14413 (40.1%) No coverage by mRNA/EST/RNASeq evidence
Caenorhabditis remanei Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 962 (3.1%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 5665 (18.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 24830 (78.9%) No coverage by mRNA/EST/RNASeq evidence
Onchocerca volvulus Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 6186 (50.6%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 5581 (45.7%) Some, but not all exon bases are covered by transcript evidence
Predicted 457 (3.7%) No coverage by mRNA/EST/RNASeq evidence
Pristionchus pacificus Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 382 (1.4%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 4992 (18.9%) Some, but not all exon bases are covered by transcript evidence
Predicted 21059 (79.7%) No coverage by mRNA/EST/RNASeq evidence
Strongyloides ratti Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 877 (7.0%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 2342 (18.8%) Some, but not all exon bases are covered by transcript evidence
Predicted 9265 (74.2%) No coverage by mRNA/EST/RNASeq evidence
Trichuris muris Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
Confirmed 6262 (41.8%) Every base of every exon has transcription evidence (mRNA/EST/RNASeq)
Partially_confirmed 3901 (26.0%) Some, but not all exon bases are covered by transcript evidence
Predicted 4832 (32.2%) No coverage by mRNA/EST/RNASeq evidence
-==============================================================================-
-=========== News for this release ============================================-
-==============================================================================-
New data sets
90 miRNA gene clusters were added from MirGeneDB 2.1
138 MirGeneDB gene cross-references added to WormBase C. elegans genes
28115 EBI AlphaFold protein cross-references added to WormBase CDSs and Proteins
New/updated reference genomes
Proposed Changes / Forthcoming Data
Model Changes
Model changes for this release are documented here:
http://wiki.wormbase.org/index.php/WS284_Models.wrm
For more information mail help@wormbase.org
-==============================================================================-
-=========== Installation guide ===============================================-
-==============================================================================-
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 50-60 Gb of disk space.
3. Obtain and install a suitable acedb binary for your system
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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