WS219
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New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010 WS219 was built by [Michael Paulini (michael.paulini@wormbase.org)] -===================================================================================- The WS219 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.WS219.gz - DNA sequences of all genes confirmed by EST &/or cDNA ii) cDNA2orf.WS219.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) iii) geneIDs.WS219.gz - list of all currentnt gene identifiers with CGC & molecular names (when known) iv) PCR_product2gene.WS219.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) wormpep219.tar.gz - full Wormpep distribution corresponding to WS219 vii) wormrna219.tar.gz - latest WormRNA release containing non-coding RNA's in the genome viii) best_blastp_hits_species.WS219.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.WS219.*.tar.gz - compressed acedb database for new release xi) models.wrm.WS219 - the latest database schema (also in above database files) xii) WS219-WS218.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 40117) ------------------------------------------ Molecular_info 38438 (95.8%) Concise_description 5692 (14.2%) Reference 14098 (35.1%) WormBase_approved_Gene_name 26062 (65%) RNAi_result 22875 (57%) Microarray_results 21042 (52.5%) SAGE_transcript 19152 (47.7%) C. elegans Wormpep data set: ---------------------------- There are 20408 CDS in autoace, 24826 when counting 4418 alternate splice forms. The 24826 sequences contain 10,921,490 base pairs in total. Modified entries 25 Deleted entries 36 New entries 101 Reappeared entries 1 Net change +66 The differnce between the total CDS's of this (24826) and the last build (24761) does not equal the net change 66 Please investigate! ! C. elegans Genome sequence composition: ---------------------------- WS219 WS218 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: ---------------------------- 169822619 total a 41799168 c 31168435 g 31196239 t 41802890 - 0 n 23855887 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 - 59500 n 2981866 Caenorhabditis brenneri Genome sequence composition: ---------------------------- 190426650 total a 52223359 c 32838518 g 32883836 t 52164943 - 0 n 20315994 Tier II Gene counts --------------------------------------------- pristionchus Gene count 29638 (Coding 29639) remanei Gene count 32431 (Coding 31476) heterorhabditis Gene count 0 (Coding 0) japonica Gene count 27177 (Coding 25870) briggsae Gene count 23043 (Coding 21995) brenneri Gene count 32295 (Coding 30707) --------------------------------------------- ------------------------------------------------- Pristionchus pacificus Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 425 (1.4%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 5309 (17.9%) Some, but not all exon bases are covered by transcript evidence Predicted 23905 (80.7%) No transcriptional evidence at all Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Pristionchus pacificus entries with WormBase-approved Gene name 2792 ------------------------------------------------- Caenorhabditis remanei Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 955 (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 24859 (79.0%) No transcriptional evidence at all Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis remanei entries with WormBase-approved Gene name 5461 ------------------------------------------------- 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 4791 ------------------------------------------------- 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 21087 (95.9%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 21708 (98.7%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis briggsae entries with WormBase-approved Gene name 5497 ------------------------------------------------- Caenorhabditis brenneri Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 1517 (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 23550 (76.7%) No transcriptional evidence at all Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis brenneri entries with WormBase-approved Gene name 3091 ------------------------------------------------- Caenorhabditis elegans Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 11654 (46.9%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10997 (44.3%) Some, but not all exon bases are covered by transcript evidence Predicted 2175 (8.8%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 24631 (99.2%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 24631 (99.2%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24430 C. elegans Operons Stats --------------------------------------------- Description: These exist as closely spaced gene clusters similar to bacterial operons --------------------------------------------- | Live Operons 1288 | | Genes in Operons 3343 | GO Annotation Stats WS219 -------------------------------------- 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 NDNo Biological Data available RCA ? TAS Traceable Author Statement ------------------------------------------------ Total number of Gene::GO connections: 262467 Genes Stats: ---------------- Genes with GO_term connections 88452 IEA GO_code present 83023 non-IEA GO_code present 5425 Source of the mapping data Source: *RNAi (GFF mapping overlaps) 23372 *citace 2133 *Inherited (motif & phenotype) 14290 GO_terms Stats: --------------- Total No. GO_terms 30467 GO_terms connected to Genes 3241 GO annotations connected with IEA 1838 GO annotations connected with non-IEA 1399 Breakdown IC - 2 IDA - 348 ISS - 126 IEP - 9 IGI - 112 IMP - 711 IPI - 68 NAS - 1 ND - 1 RCA - 0 TAS - 21 -===================================================================================- Useful Stats: --------- Genes with Sequence and CGC name WS219 46062 (24430 elegans / 5497 briggsae / 5461 remanei / 4791 japonica / 3091 brenneri / 2792 pristionchus) -===================================================================================- New Data: --------- There is a new file produced on the Sanger FTP site. requested by : Megan Senchuk, msenchuk@mcb.harvard.edu function: a 'nice' view of the phenotypes produced by genes knocked down by RNAi. script : ONTOLOGY/get_easy_phenotypes.pl output1 : ftp://ftp.sanger.ac.uk/pub/wormbase/WSXXX/ONTOLOGY/rnai_phenotypes.WSXXX.wb example lines : WBGene00001908 F17E9.9 larval arrest WBPhenotype:0000059 WBRNAi00025129|WBPaper00006395 WBGene00001908 F17E9.9 locomotion variant WBPhenotype:0000643 WBRNAi00025129|WBPaper00006395 output2 : ftp://ftp.sanger.ac.uk/pub/wormbase/WSXXX/ONTOLOGY/rnai_phenotypes_quick.WXXX.wb example lines : WBGene00001908 F17E9.9 larval arrest, locomotion variant, embryonic lethal, maternal sterile WBGene00019433 K06A5.6 embryonic lethal Genome sequence updates: ----------------------- The C.brenneri assembly had contaminations removed and was updated to the latest version available in GenBank/EMBLBank/DDBJ. New Fixes: ---------- C.brenneri genes on the removed sequences were killed. Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- ?Strain class Removed:Extended_genotype ?Variation Comment: Removed this unused tag structure as data can be stored in current tags and the additional information/context can be resolved at the display level. Model Changes: ------------------------------------ ?Molecule - fix ?Phenotype tags missed from original submission + additions (Karen Y.) ?Strain - Extended_genotype - signed off on the call, but had errors I discovered on testing. Dropped the XREF back to Variation ?Variation removal of obsolete/unused tags (Mary Ann T., Jolene F.) ?Phenotype - Migration of data from "Not" tags continues need additional tags for storing phenotypes scored but not observed (Wen C.) 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 _____________