WS223
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New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011 WS223 was built by Paul Davis -===================================================================================- The WS223 build directory includes: genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data genomes/b_malayi: - genome_feature_tables/ sequences/ genomes/c_brenneri: - genome_feature_tables/ sequences/ genomes/c_briggsae: - genome_feature_tables/ sequences/ genomes/c_elegans: - annotation/ genome_feature_tables/ sequences/ genomes/c_japonica: - genome_feature_tables/ sequences/ genomes/c_remanei: - genome_feature_tables/ sequences/ genomes/h_bacteriophora: - genome_feature_tables/ sequences/ genomes/h_contortus: - genome_feature_tables/ sequences/ genomes/m_hapla: - genome_feature_tables/ sequences/ genomes/m_incognita: - sequences/ genomes/p_pacificus: - genome_feature_tables/ sequences/ *annotation/ - contains additional annotations i) confirmed_genes.WS223.gz - DNA sequences of all genes confirmed by EST &/or cDNA ii) cDNA2orf.WS223.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) iii) geneIDs.WS223.gz - list of all current gene identifiers with CGC & molecular names (when known) iv) PCR_product2gene.WS223.gz - Mappings between PCR products and overlapping Genes v) oligo_mapping.gz - V *genome_feature_tables/ - contains the main .gff files and supplementary .gff data *sequences/ - contains dna/ protein/ rna/ sub dirs sequences/protein - WormBase protein set for species + history etc. vi) wormpep223.tar.gz - full Wormpep distribution corresponding to WS223 vii) wormrna223.tar.gz - latest WormRNA release containing non-coding RNA's in the genome viii) best_blastp_hits_species.WS223.gz - for each C. elegans WormPep protein, lists Best blastp match to human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins. sequences/dna - WormBase dna data genomic sequence (raw, soft_masked masked), agp ix) intergenic_sequences.dna.gz sequences/rna - WormBase rna gene data. acedb DIR - Everything needed to generate a local copy of the The Primary database x) database.WS223.*.tar.gz - compressed acedb database for new release xi) models.wrm.WS223 - the latest database schema (also in above database files) xii) WS223-WS222.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 - compara.tar.bz2 wormpep217_clw.sql.bz2 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 47388) ------------------------------------------ Molecular_info 45719 (96.5%) Concise_description 5726 (12.1%) Reference 14134 (29.8%) WormBase_approved_Gene_name 26110 (55.1%) RNAi_result 24631 (52%) Microarray_results 22112 (46.7%) SAGE_transcript 19172 (40.5%) C. elegans Wormpep data set: ---------------------------- There are 20431 CDS in autoace, 24959 when counting 4528 alternate splice forms. The 24959 sequences contain 10,959,918 base pairs in total. Modified entries 165 Deleted entries 17 New entries 38 Reappeared entries 7 Net change +28 The differnce between the total CDS's of this (24959) and the last build (24938) does not equal the net change 28 Please investigate! ! C. elegans Genome sequence composition: ---------------------------- WS223 WS222 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: ---------------------------- 163282347 total a 39053092 c 25603225 g 25576971 t 39126103 - 0 n 33922956 Caenorhabditis briggsae Genome sequence composition: ---------------------------- 108478630 total a 33004189 c 19675861 g 19707411 t 33049803 - 0 n 3041366 Caenorhabditis brenneri Genome sequence composition: ---------------------------- 190487923 total a 52239259 c 32853644 g 32897666 t 52181360 - 0 n 20315994 Tier II Gene counts --------------------------------------------- pristionchus Gene count 24216 (Coding 24216) remanei Gene count 32431 (Coding 31471) heterorhabditis Gene count 0 (Coding 0) japonica Gene count 27177 (Coding 25870) briggsae Gene count 23038 (Coding 21967) brenneri Gene count 32260 (Coding 30670) --------------------------------------------- ------------------------------------------------- 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 3077 ------------------------------------------------- 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 5495 ------------------------------------------------- Caenorhabditis japonica Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 1182 (4.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 4974 (19.2%) Some, but not all exon bases are covered by transcript evidence Predicted 19714 (76.2%) No transcriptional evidence at all Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis japonica entries with WormBase-approved Gene name 4831 ------------------------------------------------- Caenorhabditis briggsae Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 52 (0.2%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 856 (3.9%) Some, but not all exon bases are covered by transcript evidence Predicted 21083 (95.9%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 21703 (98.7%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis briggsae entries with WormBase-approved Gene name 5542 ------------------------------------------------- Caenorhabditis brenneri Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 1512 (4.9%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 5635 (18.4%) Some, but not all exon bases are covered by transcript evidence Predicted 23526 (76.7%) No transcriptional evidence at all Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis brenneri entries with WormBase-approved Gene name 3119 ------------------------------------------------- Caenorhabditis elegans Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 11759 (47.1%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11022 (44.2%) Some, but not all exon bases are covered by transcript evidence Predicted 2178 (8.7%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 24602 (98.6%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 24760 (99.2%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24486 C. elegans Operons Stats --------------------------------------------- Description: These exist as closely spaced gene clusters similar to bacterial operons --------------------------------------------- | Live Operons 1288 | | Genes in Operons 3342 | --------------------------------------------- GO Annotation Stats WS223 -------------------------------------- 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: 259979 Genes Stats: ---------------- Genes with GO_term connections 87264 IEA GO_code present 81404 non-IEA GO_code present 5856 Source of the mapping data Source: *RNAi (GFF mapping overlaps) 24450 *citace 2224 *Inherited (motif & phenotype) 15098 GO_terms Stats: --------------- Total No. GO_terms 30478 GO_terms connected to Genes 3298 GO annotations connected with IEA 1856 GO annotations connected with non-IEA 1437 Breakdown IC - 3 IDA - 356 ISS - 130 IEP - 9 IGI - 116 IMP - 732 IPI - 69 NAS - 1 ND - 1 RCA - 0 TAS - 20 -===================================================================================- Useful Stats: --------- Genes with Sequence and CGC name WS223 46550 (24486 elegans / 5542 briggsae / 5495 remanei / 4831 japonica / 3119 brenneri / 3077 pristionchus) -===================================================================================- New Data: --------- Details of 775 wild isolate strains stored at the Felix lab have been curated. This is the first of such datasets and we continue to work on incorporating information about wild isolate strains stored in other worm laboratories. Specific isolation information is included. Genome sequence updates: ----------------------- New Fixes: ---------- Phenotypes "Not" observed: The Phenotype observed NOT data model has been retired as this proved confusing to our users. Old Phenotype "WBPhenotype:0000216" Not New Phenotype_not_observed "WBPhenotype:0000216" Remark "AC\/VU specification normal" Known Problems: --------------- Other Changes: -------------- Caenorhabditis sp. 3 PS1010 is now Caenorhabditis angaria. WormBase will be working to accommodate this change on our ftp and www sites. http://www.ingentaconnect.com/content/brill/nemy/2011/00000013/00000001/art00007 Proposed Changes / Forthcoming Data: ------------------------------------- WS224 will include over 20,000 new SNPs from WGS. The data was published in PMID 20439776 Sarin S et al. (2010) Genetics "Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis ...." This data has also been submitted to dbSNP. We are expecting to see a massive increase in this sort of data. WS224 will contain the new cb4 C. briggsae assembly. This will require the revision of any gene model that overlaps the rearrangements in the assembly. Model Changes: ------------------------------------ Simple additions were made to the Transposon_family and Strain classes The Picture class was substantially re-worked Small additional changes that should have gone in before. Additional information can be found here: http://wiki.wormbase.org/index.php/WS223_Models.wrm For more info mail worm@sanger.ac.uk -===================================================================================- 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 _____________