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| − | New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008
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| − | WS196 was built by Mary Ann and Anthony
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| − | ======================================================================
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| − | This directory includes:
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| − | i) database.WS196.*.tar.gz - compressed data for new release
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| − | ii) models.wrm.WS196 - the latest database schema (also in above database files)
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| − | iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome)
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| − | iv) WS196-WS195.dbcomp - log file reporting difference from last release
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| − | v) wormpep196.tar.gz - full Wormpep distribution corresponding to WS196
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| − | vi) wormrna196.tar.gz - latest WormRNA release containing non-coding RNA's in the genome
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| − | vii) confirmed_genes.WS196.gz - DNA sequences of all genes confirmed by EST &/or cDNA
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| − | viii) cDNA2orf.WS196.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA)
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| − | ix) gene_interpolated_map_positions.WS196.gz - Interpolated map positions for each coding/RNA gene
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| − | x) clone_interpolated_map_positions.WS196.gz - Interpolated map positions for each clone
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| − | xi) best_blastp_hits.WS196.gz - for each C. elegans WormPep protein, lists Best blastp match to
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| − | human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.
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| − | xii) best_blastp_hits_brigprot.WS196.gz - for each C. briggsae protein, lists Best blastp match to
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| − | human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
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| − | xiii) geneIDs.WS196.gz - list of all current gene identifiers with CGC & molecular names (when known)
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| − | xiv) PCR_product2gene.WS196.gz - Mappings between PCR products and overlapping Genes
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| − | Release notes on the web:
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| − | -------------------------
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| − | http://www.wormbase.org/wiki/index.php/Release_Schedule
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| − | Genome sequence composition:
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| − | ----------------------------
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| − | WS196 WS195 change
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| − | ----------------------------------------------
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| − | a 32365950 32365950 +0
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| − | c 17779889 17779889 +0
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| − | g 17756041 17756041 +0
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| − | t 32365753 32365753 +0
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| − | n 0 0 +0
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| − | - 0 0 +0
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| − |
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| − | Total 100267633 100267633 +0
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| − | Chromosomal Changes:
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| − | --------------------
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| − | There are no changes to the chromosome sequences in this release.
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| − | Gene data set (Live C.elegans genes 29872)
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| − | ------------------------------------------
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| − | Molecular_info 28155 (94.3%)
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| − | Concise_description 5447 (18.2%)
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| − | Reference 13254 (44.4%)
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| − | WormBase_approved Gene name 15636 (52.3%)
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| − | RNAi_result 20799 (69.6%)
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| − | Microarray_results 20438 (68.4%)
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| − | SAGE_transcript 18838 (63.1%)
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| − | Wormpep data set:
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| − | ----------------------------
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| − |
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| − | There are 20191 CDS in autoace, 23902 when counting 3711 alternate splice forms.
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| − | The 23902 sequences contain 10,518,004 base pairs in total.
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| − |
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| − | Modified entries 66
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| − | Deleted entries 25
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| − | New entries 21
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| − | Reappeared entries 0
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| − | Net change -4
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| − | Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
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| − | -------------------------------------------------
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| − | Confirmed 8517 (35.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)
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| − | Partially_confirmed 10985 (46.0%) Some, but not all exon bases are covered by transcript evidence
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| − | Predicted 4400 (18.4%) No transcriptional evidence at all
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| − | Status of entries: Protein Accessions
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| − | -------------------------------------
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| − | UniProtKB accessions 23768 (99.4%)
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| − | Status of entries: Protein_ID's in EMBL
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| − | ---------------------------------------
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| − | Protein_id 23772 (99.5%)
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| − |
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| − | Gene <-> CDS,Transcript,Pseudogene connections
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| − | ----------------------------------------------
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| − | Caenorhabditis elegans entries with WormBase-approved Gene name 13967
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| − | GeneModel correction progress WS195 -> WS196
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| − | -----------------------------------------
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| − | Confirmed introns not in a CDS gene model;
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| − |
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| − | +---------+--------+
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| − | | Introns | Change |
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| − | +---------+--------+
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| − | Cambridge | 40 | 13 |
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| − | St Louis | 118 | 15 |
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| − | +---------+--------+
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| − |
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| − |
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| − | Members of known repeat families that overlap predicted exons;
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| − |
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| − | +---------+--------+
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| − | | Repeats | Change |
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| − | +---------+--------+
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| − | Cambridge | 6 | 0 |
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| − | St Louis | 6 | 0 |
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| − | +---------+--------+
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| − |
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| − |
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| − | Synchronisation with GenBank / EMBL:
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| − | ------------------------------------
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| − | No synchronisation issues
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| − | There are no gaps remaining in the genome sequence
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| − | ---------------
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| − | For more info mail worm@sanger.ac.uk
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| − | -===================================================================================-
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| − |
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| − |
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| − | New Data:
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| − | ---------
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| − | This release includes the C. brenneri genome for the first time. Orthologies to the other species in WormBase have been determined and Gene names transferred from C. elegans where appropriate.
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| − |
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| − | There has been some manual correction of the C. briggsae nGASP gene predictions.
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| − | Precalculated protein alignments are now made for each main WormBase species.
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| − | This is available on the Sanger FTP site ftp.sanger.ac.uk/pub2/wormbase/live_release/wormpep_clw.sql.bz2 . For info contact WormBase.
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| − | Genome sequence updates:
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| − | -----------------------
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| − |
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| − | New Fixes:
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| − | ----------
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| − |
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| − |
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| − | Known Problems:
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| − | ---------------
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| − | Due to the amounts of data and time pressures to get C. brenneri in this release we didn't have time to load all of the blast hits for every species.
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| − | They are still available in the GFF files and so visible in the genome browser but not via querying the acedb database.
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| − |
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| − | Other Changes:
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| − | --------------
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| − | Proposed Changes / Forthcoming Data:
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| − | -------------------------------------
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| − |
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| − |
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| − |
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| − | Model Changes:
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| − | ------------------------------------
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| − | added Person to #Affiliation
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| − | -===================================================================================-
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| − | Quick installation guide for UNIX/Linux systems
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| − | -----------------------------------------------
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| − | 1. Create a new directory to contain your copy of WormBase,
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| − | e.g. /users/yourname/wormbase
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| − | 2. Unpack and untar all of the database.*.tar.gz files into
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| − | this directory. You will need approximately 2-3 Gb of disk space.
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| − | 3. Obtain and install a suitable acedb binary for your system
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| − | (available from www.acedb.org).
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| − | 4. Use the acedb 'xace' program to open your database, e.g.
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| − | type 'xace /users/yourname/wormbase' at the command prompt.
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| − | 5. See the acedb website for more information about acedb and
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| − | using xace.
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| − | ____________ END _____________
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