From WormBaseWiki
Jump to navigationJump to search

 new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007
 WS176 was built by Mary Ann Tuli
 This directory includes:
 i)   database.WS176.*.tar.gz    -   compressed data for new release
 ii)  models.wrm.WS176           -   the latest database schema (also in above database files)
 iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
 iv)  WS176-WS175.dbcomp         -   log file reporting difference from last release
 v)   wormpep176.tar.gz          -   full Wormpep distribution corresponding to WS176
 vi)   wormrna176.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
 vii)  confirmed_genes.WS176.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
 viii) cDNA2orf.WS176.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
 ix)   gene_interpolated_map_positions.WS176.gz    - Interpolated map positions for each coding/RNA gene
 x)    clone_interpolated_map_positions.WS176.gz   - Interpolated map positions for each clone
 xi)   best_blastp_hits.WS176.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.WS176.gz   - for each C. briggsae protein, lists Best blastp match to
                                      human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
 xiii) geneIDs.WS176.gz   - list of all current gene identifiers with CGC & molecular names (when known)
 xiv)  PCR_product2gene.WS176.gz   - Mappings between PCR products and overlapping Genes
 Release notes on the web:
 Genome sequence composition:
         WS175           WS174           change
 a       32365889        32365889          +0
 c       17779856        17779856          +0
 g       17756016        17756016          +0
 t       32365689        32365689          +0
 n       0               0                 +0
 Total   100267450       100267450         +0
 Chromosomal Changes:
 There are no changes to the chromosome sequences in this release.
 Gene data set (Live C.elegans genes 24101)
 Molecular_info              22410 (93%)
 Concise_description          4578 (19%)
 Reference                    7003 (29.1%)
 CGC_approved Gene name       9213 (38.2%)
 RNAi_result                 19876 (82.5%)
 Microarray_results          19152 (79.5%)
 SAGE_transcript             20034 (83.1%)
 Wormpep data set:
 There are 20131 CDS in autoace, 23375 when counting 3244 alternate  splice forms.
 The 23375 sequences contain 10,266,608 base pairs in total.
 Modified entries              91
 Deleted entries               77
 New entries                  175
 Reappeared entries             4
 Net change  +102
 Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 Confirmed              7940 (34.0%)     Every base of every exon has transcription evidence (mRNA, EST etc.)
 Partially_confirmed   10811 (46.3%)     Some, but not all exon bases are covered by transcript evidence
 Predicted              4624 (19.8%)     No transcriptional evidence at all
 Status of entries: Protein Accessions
 UniProtKB/Swiss-Prot accessions   3523 (15.1%)
 UniProtKB/TrEMBL accessions     19412 (83.0%)
 Status of entries: Protein_ID's in EMBL
 Protein_id            22935 (98.1%)
 Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
 Entries with CGC-approved Gene name   7573
 GeneModel correction progress WS175 -> WS176
 Confirmed introns not in a CDS gene model;
                 | Introns | Change |
 Cambridge       |     70  |  -103  |
 St Louis        |    179  |   -33  |
 Members of known repeat families that overlap predicted exons;
                 | Repeats | Change |
 Cambridge       |      6  |     0  |
 St Louis        |      6  |     0  |
 Synchronisation with GenBank / EMBL:
 No synchronisation issues
 There are no gaps remaining in the genome sequence
 For more info mail
 New Data:
  A set of 51,623 mass spectroscopy peptides from Gennifer Merrihew at Michael MacCoss's laboratory
 has been added to this release.  Proteins have been fragmented and the molecular weights of the
 fragments have then been used to deduce the sequence of the fragments by comparing to a database
 of C. elegans protein sequences.
  The peptides were mapped to the genome using the known positions of the peptides in the matching
 proteins and the known positions of the proteins' genes on the genome.
  This data gives confirmatory evidence of many exons and (where they span splice sites) some introns.
 Genome sequence updates:
 New Fixes:
 Known Problems:
 Other Changes:
 Proposed Changes / Forthcoming Data:
 A number of genomic canonical clones are going to be updated for WS177.
 F54F7   deletion  tagctcaccagcttgcacgGgaagtgaaagtcttgaaata
 F28H7   deletion  aacaaaatcttgcaactagTaatgtgaaaaagtgtggact
 K07A1   insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt
 F13G3   insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg
 R10E11  deletion  gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta
 07A1   insertion ttctcaaatttcagtttatTggaacattacaaatatgtgt
 F13G3   insertion tttttttcagacaccgttcgtttggctccgGcgcgatcaacatggtgatggttgcacaagg
 R10E11  deletion  gccacctggaaatcaatcagctcctcaaaaAgaattccgaatctgcctatattctgttcta
 K11H3   insertion gcattaacaacacacggaaatcgaaatggaCcacttcgttatagtcttcttcaacaacgag
 F13G3   insertion ccttgtgcaaccatcaccatgttgatcgcgGcggagccaaacgaacggtgtctgaaaaaaa
 Y95D11A shift-overlap with F49D11
 Model Changes:
 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
 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 _____________