WS225
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Jump to navigationJump to searchNew release of WormBase WS225, Wormpep225 and Wormrna225 Tue Apr 5 11:57:03 BST 2011 WS225 was built by klh -===================================================================================- The WS225 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.WS225.gz - DNA sequences of all genes confirmed by EST &/or cDNA ii) cDNA2orf.WS225.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) iii) geneIDs.WS225.gz - list of all current gene identifiers with CGC & molecular names (when known) iv) PCR_product2gene.WS225.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) wormpep225.tar.gz - full Wormpep distribution corresponding to WS225 vii) wormrna225.tar.gz - latest WormRNA release containing non-coding RNA's in the genome viii) best_blastp_hits_species.WS225.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.WS225.*.tar.gz - compressed acedb database for new release xi) models.wrm.WS225 - the latest database schema (also in above database files) xii) WS225-WS224.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 47390) ------------------------------------------ Molecular_info 45720 (96.5%) Concise_description 5741 (12.1%) Reference 14138 (29.8%) WormBase_approved_Gene_name 26143 (55.2%) RNAi_result 24630 (52%) Microarray_results 22114 (46.7%) SAGE_transcript 19135 (40.4%) C. elegans Wormpep data set: ---------------------------- There are 20431 CDS in autoace, 25030 when counting 4599 alternate splice forms. The 25030 sequences contain 10,991,449 base pairs in total. Modified entries 40 Deleted entries 17 New entries 37 Reappeared entries 2 Net change +22 The differnce between the total CDS's of this (25030) and the last build (25010) does not equal the net change 22 Please investigate! ! C. elegans Genome sequence composition: ---------------------------- WS225 WS224 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: ---------------------------- 108419768 total a 32984239 c 19684682 g 19693545 t 33054090 - 0 n 3003212 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) japonica Gene count 27177 (Coding 25870) briggsae Gene count 23051 (Coding 21963) brenneri Gene count 32259 (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 3085 ------------------------------------------------- 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 5517 ------------------------------------------------- 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 4848 ------------------------------------------------- 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 854 (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 21683 (98.6%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis briggsae entries with WormBase-approved Gene name 5563 ------------------------------------------------- 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 3136 ------------------------------------------------- Caenorhabditis elegans Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 11526 (46.0%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11320 (45.2%) Some, but not all exon bases are covered by transcript evidence Predicted 2184 (8.7%) No transcriptional evidence at all Status of entries: Protein Accessions ------------------------------------- UniProtKB accessions 24691 (98.6%) Status of entries: Protein_ID's in EMBL --------------------------------------- Protein_id 24846 (99.3%) Gene <-> CDS,Transcript,Pseudogene connections ---------------------------------------------- Caenorhabditis elegans entries with WormBase-approved Gene name 24521 C. elegans Operons Stats --------------------------------------------- Description: These exist as closely spaced gene clusters similar to bacterial operons --------------------------------------------- | Live Operons 1287 | | Genes in Operons 3336 | --------------------------------------------- GO Annotation Stats WS225 -------------------------------------- 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: 251965 Genes Stats: ---------------- Genes with GO_term connections 86464 IEA GO_code present 80577 non-IEA GO_code present 5883 Source of the mapping data Source: *RNAi (GFF mapping overlaps) 24514 *citace 2288 *Inherited (motif & phenotype) 15098 GO_terms Stats: --------------- Total No. GO_terms 30490 GO_terms connected to Genes 3368 GO annotations connected with IEA 1859 GO annotations connected with non-IEA 1502 Breakdown IC - 3 IDA - 392 ISS - 137 IEP - 9 IGI - 124 IMP - 741 IPI - 73 NAS - 1 ND - 1 RCA - 0 TAS - 20 -===================================================================================- Useful Stats: --------- Genes with Sequence and CGC name WS225 46670 (24521 elegans / 5563 briggsae / 5517 remanei / 4848 japonica / 3136 brenneri / 3085 pristionchus) -===================================================================================- New Data: --------- New genome: Trichinella spiralis The newly released Trichinella spiralis genome and associated gene set (Mitreva et.al, Nature Genetics 43, 228-235(2011)) has been imported into WormBase from the public nucleotide archive (ENA accession ABIR00000000). Orthology to the genes of C.elegans, C.briggsae, C.remanei, C.brenneri, C.japonica and P.pacificus has been derived using Compara analysis. T.spiralis Genes have been assigned provisional CGC names based on their C.elegans orthologs. GERP sequence conservation and PECAN whole genome alignments have also been added to the available comparative data. Genome sequence updates: ----------------------- New Fixes: ---------- Known Problems: --------------- Other Changes: -------------- Proposed Changes / Forthcoming Data: ------------------------------------- Model Changes: ------------------------------------ WS225 sees the introduction of the WBProcess model. For more info mail hinxton@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 _____________
Patches
ftp.sanger.ac.uk/pub2/wormbase/WS225/acedb/patches/BLAT_Homol.patch.ace.gz
ftp.sanger.ac.uk/pub2/wormbase/WS225/acedb/patches/gene_confirmation_status.ace.gz
These patches address a bug causing a small number of BLAT alignments to be missing from the GFF dumps, and the consequent slight under-calling of the number of confirmed CDSs. Wormpep and GFF files were patched on the FTP site at 11th April 2011 15.30GMT
After applying the patches, the breakdown is as follows:
------------------------------------------------- Caenorhabditis elegans Protein Stats: ------------------------------------------------- Status of entries: Confidence level of prediction (based on the amount of transcript evidence) ------------------------------------------------- Confirmed 11820 (47.2%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 11320 (44.1%) Some, but not all exon bases are covered by transcript evidence Predicted 2184 (8.7%) No transcriptional evidence at all