WS289
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WS288 was built by Stavros Diamantakis with the input from the WormBase Community and Team. Thank you!
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-========= FTP site structure =================================================-
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The WS288 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.WS288.genomic.fa.gz - Unmasked genomic DNA
- G_SPECIES.BIOPROJECT.WS288.genomic_masked.fa.gz - Hard-masked (repeats replaced with Ns) genomic DNA
- G_SPECIES.BIOPROJECT.WS288.genomic_softmasked.fa.gz - Soft-masked (repeats lower-cased) genomic DNA
- G_SPECIES.BIOPROJECT.WS288.protein.fa.gz - Current live protein set
- G_SPECIES.BIOPROJECT.WS288.CDS_transcripts.fa.gz - Spliced cDNA sequence for the CDS portion of protein-coding transcripts
- G_SPECIES.BIOPROJECT.WS288.mRNA_transcripts.fa.gz - Spliced cDNA sequence for the full-length (including UTRs) mRNA for transcripts
- G_SPECIES.BIOPROJECT.WS288.ncrna_transcripts.fa.gz - Spliced cDNA sequence for non-coding RNA transcripts
- G_SPECIES.BIOPROJECT.WS288.pseudogenic_transcripts.fa.gz - Spliced cDNA sequence for pseudogenic transcripts
- G_SPECIES.BIOPROJECT.WS288.transposon_transcripts.fa.gz - Spliced cDNA sequence for mRNAs and pseudogenes located in Transposons
- G_SPECIES.BIOPROJECT.WS288.transposons.fa.gz - DNA sequence of curated and predicted Transposons
- G_SPECIES.BIOPROJECT.WS288.transposon_cds.pep.gz - Protein sequence of curated CDSs associated with Transposons
- G_SPECIES.BIOPROJECT.WS288.intergenic_sequences.fa.gz - DNA sequence between pairs of adjacent genes
- G_SPECIES.BIOPROJECT.WS288.annotations.gff[2|3].gz - Sequence features in either GFF2 or GFF3 format
- G_SPECIES.BIOPROJECT.WS288.protein_annotation.gff3.gz - Sequence features in proteins in GFF3 format
- G_SPECIES.BIOPROJECT.WS288.canonical_geneset.gtf.gz - Genes, transcripts and CDSs in GTF (GFF2) format
- G_SPECIES.BIOPROJECT.WS288.ests.fa.gz - ESTs and mRNA sequences extracted from the public databases
- G_SPECIES.BIOPROJECT.WS288.best_blastp_hits.txt.gz - Best blastp matches to human, fly, yeast, and non-WormBase Uniprot proteins
- G_SPECIES.BIOPROJECT.WS288.*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.WS288.confirmed_genes.txt.gz - DNA sequences of all genes confirmed by EST &/or cDNA
- G_SPECIES.BIOPROJECT.WS288.cDNA2orf.txt.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
- G_SPECIES.BIOPROJECT.WS288.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known)
- G_SPECIES.BIOPROJECT.WS288.PCR_product2gene.txt.gz - Mappings between PCR products and overlapping Genes
- G_SPECIES.BIOPROJECT.WS288.*oligo_mapping.txt.gz - Oligo array mapping files
- G_SPECIES.BIOPROJECT.WS288.knockout_consortium_alleles.xml.gz - Table of Knockout Consortium alleles
- G_SPECIES.BIOPROJECT.WS288.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
- G_SPECIES.BIOPROJECT.WS288.TSS.wig.tar.gz - Wiggle plot files of Transcription Start Sites from the papers WBPaper00042246, WBPaper00042529, WBPaper00042354
- G_SPECIES.BIOPROJECT.WS288.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.WS288.*.tar.gz - compressed acedb database for new release
- models.wrm.WS288 - the latest database schema (also in above database files)
- WS288-WS287.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.WS288.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:
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http://www.wormbase.org/about/release_schedule
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-=========== C. elegans data summary =================================================-
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Genome version
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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 (49177 genes in total)
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Protein-coding (19984 genes):
Curated description 5098 (25.5%)
Automated description 19874 (99.4%)
Human disease association 3388 (17.0%)
Approved Gene name 10769 (53.9%)
Reference 11827 (59.2%)
RNAi results 18344 (91.8%)
Microarray results 19776 (99.0%)
Expression patterns 19648 (98.3%)
Variations 19980 (100.0%)
Interaction data 16200 (81.1%)
Non-coding RNA and pseudogene (27668 genes):
Curated description 219 (0.8%)
Automated description 8858 (32.0%)
Human disease association 16 (0.1%)
Approved Gene name 16526 (59.7%)
Reference 5952 (21.5%)
RNAi results 861 (3.1%)
Microarray results 2267 (8.2%)
Expression patterns 899 (3.2%)
Variations 27632 (99.9%)
Interaction data 941 (3.4%)
Uncloned (1525 genes):
Curated description 778 (51.0%)
Automated description 116 (7.6%)
Human disease association 10 (0.7%)
Approved Gene name 1524 (99.9%)
Reference 1124 (73.7%)
RNAi results 0 (0.0%)
Microarray results 0 (0.0%)
Expression patterns 18 (1.2%)
Variations 1184 (77.6%)
Interaction data 122 (8.0%)
Wormpep data set:
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There are 28564 CDSs, from 19981 protein-coding loci
The 28564 sequences contain 40758087 base pairs in total.
Modified entries 1
Deleted entries 5
New entries 2
Reappeared entries 1
Net change -2
C. elegans Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
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Confirmed 23532 (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
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Live Operons 1385
Genes in Operons 3688
C. elegans GO annotation status
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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 126735
Breakdown by annotation provider:
WormBase 18749
UniProt 52222
GO_Central 28770
InterPro 20895
IntAct 2399
GOC 2329
RHEA 1156
SynGO 68
CACAO 35
ParkinsonsUK-UCL 30
MGI 29
BHF-UCL 23
HGNC-UCL 14
CAFA 7
DisProt 5
ARUK-UCL 2
HGNC 1
FlyBase 1
Breakdown by evidence code:
IEA 67031
Interpro2GO 20895
Other 46136
non-IEA 59704
EXP 2
HDA 386
HEP 320
IBA 28749
IC 117
IDA 7874
IEP 169
IGI 4671
IKR 5
IMP 10426
IPI 4274
ISM 9
ISO 1
ISS 1906
NAS 180
ND 429
RCA 13
TAS 173
Genes Stats:
Genes with GO_term connections 14217
Non-IEA-only annotation 1380
IEA-only annotation 4879
Both IEA and non-IEA annotations 7958
GO_term Stats:
Distinct GO_terms connected to Genes 7030
Associated by non-IEA only 3900
Associated by IEA only 835
Associated by both IEA and non-IEA 2295
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-=========== Other core species data summary =================================-
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Assembly versions
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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
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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
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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 12977 (12464 coding)
Trichuris muris 15755 (14995 coding)
Brugia malayi Gene model confirmation status (based on the EST/mRNA/RNASeq evidence)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
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-=========== News for this release ============================================-
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New data sets
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New/updated reference genomes
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Proposed Changes / Forthcoming Data
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Model Changes
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Model changes for this release are documented here:
http://wiki.wormbase.org/index.php/WS288_Models.wrm
For more information mail help@wormbase.org
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