WS180

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 New release of WormBase WS180, Wormpep180 and Wormrna180 Fri Aug 17 13:41:37 BST 2007
 
 
 WS180 was built by Anthony
 ======================================================================
 
 This directory includes:
 i)   database.WS180.*.tar.gz    -   compressed data for new release
 ii)  models.wrm.WS180           -   the latest database schema (also in above database files)
 iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
 iv)  WS180-WS179.dbcomp         -   log file reporting difference from last release
 v)   wormpep180.tar.gz          -   full Wormpep distribution corresponding to WS180
 vi)   wormrna180.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
 vii)  confirmed_genes.WS180.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
 viii) cDNA2orf.WS180.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
 ix)   gene_interpolated_map_positions.WS180.gz    - Interpolated map positions for each coding/RNA gene
 x)    clone_interpolated_map_positions.WS180.gz   - Interpolated map positions for each clone
 xi)   best_blastp_hits.WS180.gz  - for each C. elegans WormPep protein, lists Best blastp match to
                             human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.
 xii)  best_blastp_hits_brigprot.WS180.gz   - for each C. briggsae protein, lists Best blastp match to
                                      human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
 xiii) geneIDs.WS180.gz   - list of all current gene identifiers with CGC & molecular names (when known)
 xiv)  PCR_product2gene.WS180.gz   - Mappings between PCR products and overlapping Genes
 
 
 Release notes on the web:
 -------------------------
 http://www.wormbase.org/wiki/index.php/Release_notes
 
 
 
 Genome sequence composition:
 ----------------------------
 
         WS180           WS179           change
 ----------------------------------------------
 a       32365949        32365888         +61
 c       17779887        17779857         +30
 g       17756036        17756016         +20
 t       32365750        32365689         +61
 n       0               0                 +0
 -       0               0                 +0
 
 Total   100267622       100267450       +172
 Total number of bases has increased due to a sequence update for clone CTEL3X.
 
 
 Chromosomal Changes:
 --------------------
 
 Chromosome: V
 559 558 0   ->   559 730 172
 
 
 Gene data set (Live C.elegans genes 29500)
 ------------------------------------------
 Molecular_info              27792 (94.2%)
 Concise_description          4851 (16.4%)
 Reference                    7212 (24.4%)
 CGC_approved Gene name       14707 (49.9%)
 RNAi_result                 20691 (70.1%)
 Microarray_results          19946 (67.6%)
 SAGE_transcript             18642 (63.2%)
 
 
 
 
 Wormpep data set:
 ----------------------------
 
 There are 20145 CDS in autoace, 23511 when counting 3366 alternate splice forms.
 
 The 23511 sequences contain  base pairs in total.
 
 Modified entries      100
 Deleted entries       0
 New entries           79
 Reappeared entries    0
 
 Net change  +79
 
 Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 -------------------------------------------------
 Confirmed              8135 (34.6%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
 Partially_confirmed   10717 (45.6%)     Some, but not all exon bases are covered by transcript evidence
 Predicted              4659 (19.8%)     No transcriptional evidence at all
 
 
 
 Status of entries: Protein Accessions
 -------------------------------------
 UniProtKB/Swiss-Prot accessions   3556 (15.1%)
 UniProtKB/TrEMBL accessions     19592 (83.3%)
 
 
 
 Status of entries: Protein_ID's in EMBL
 ---------------------------------------
 Protein_id            23157 (98.5%)
 
 
 
 Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
 ---------------------------------------------
 Entries with CGC-approved Gene name  13082
 
 
 GeneModel correction progress WS179 -> WS180
 -----------------------------------------
 Confirmed introns not in a CDS gene model
 (these changes represent a bug fix in the intron code)
 
                 +---------+--------+
                 | Introns | Change |
                 +---------+--------+
 Cambridge       |     23  |  -3520  |
 St Louis        |    158  |  -3398  |
                 +---------+--------+
 
 
 Members of known repeat families that overlap predicted exons;
 
                 +---------+--------+
                 | Repeats | Change |
                 +---------+--------+
 Cambridge       |      6  |     0  |
 St Louis        |      6  |     0  |
                 +---------+--------+
 
 
 
 Synchronisation with GenBank / EMBL:
 ------------------------------------
 
 There are no gaps remaining in the genome sequence
 ---------------
 For more info mail help@wormbase.org
 -===================================================================================-
 
 
 
 New Data:
 ---------
 5356 21uRNA genes described in Ruby et al Cell 127, 1193-1207 are included.
 The elegans-briggsae waba alignments have been remade based on the chromosomal sequences for each species
 The protein sets from Uniprot(SwissProt and TrEMBL) used for blast analyses have been updated to versions 54 and 37 respectively.
 OMIM orthologs and homology groups are now included.
 Orthologs from Hillier LW et al. (2007) PLoS Biol "Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive ...."
 are incorporated.
 
 Genome sequence updates:
 -----------------------
 172 bases were added to cTel3X
 
 New Fixes:
 ----------
 There has been some confusion with the waba data being a mixture of that run on chromosomes and clone sequences which has been
 resolved.
 
 Known Problems:
 ---------------
 
 
 Other Changes:
 --------------
 
 Proposed Changes / Forthcoming Data:
 -------------------------------------
 
 
 Model Changes:
 ------------------------------------
 Changes to Variation class to handle CGH data.  Natural_variation tag for marking natural variation and CGH_deleted_probes for
 marking the outermost positions of the definitely deleted region
 
 -===================================================================================-
 
 
 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.
 
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