WS171

From WormBaseWiki
Jump to: navigation, search
New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb  8 15:28:27 GMT 2007
 
 
 WS171 was built by Anthony
 ======================================================================
 
 This directory includes:
 i)   database.WS171.*.tar.gz    -   compressed data for new release
 ii)  models.wrm.WS171           -   the latest database schema (also in above database files)
 iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
 iv)  WS171-WS170.dbcomp         -   log file reporting difference from last release
 v)   wormpep171.tar.gz          -   full Wormpep distribution corresponding to WS171
 vi)   wormrna171.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
 vii)  confirmed_genes.WS171.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
 viii) cDNA2orf.WS171.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
 ix)   gene_interpolated_map_positions.WS171.gz    - Interpolated map positions for each coding/RNA gene
 x)    clone_interpolated_map_positions.WS171.gz   - Interpolated map positions for each clone
 xi)   best_blastp_hits.WS171.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.WS171.gz   - for each C. briggsae protein, lists Best blastp match to
                                      human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
 xiii) geneIDs.WS171.gz   - list of all current gene identifiers with CGC & molecular names (when known)
 xiv)  PCR_product2gene.WS171.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:
 ----------------------------
 
        	WS171       	WS170      	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 23967)
 ------------------------------------------
 Molecular_info              22274 (92.9%)
 Concise_description          4401 (18.4%)
 Reference                    6731 (28.1%)
 CGC_approved Gene name       8945 (37.3%)
 RNAi_result                 19843 (82.8%)
 Microarray_results          19135 (79.8%)
 SAGE_transcript             20061 (83.7%)
 
 
 
 
 Wormpep data set:
 ----------------------------
 
 There are 20085 CDS in autoace, 23226 when counting 3141 alternate splice forms.
 
 The 23226 sequences contain 10,187,058 base pairs in total.
 
 Modified entries               6
 Deleted entries                4
 New entries                    3
 Reappeared entries             3
 
 Net change  +2
 
 
 
 Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 -------------------------------------------------
 Confirmed              7825 (33.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
 Partially_confirmed   10745 (46.3%)	Some, but not all exon bases are covered by transcript evidence
 Predicted              4656 (20.0%)	No transcriptional evidence at all
 
 
 
 Status of entries: Protein Accessions
 -------------------------------------
 UniProtKB/Swiss-Prot accessions   3489 (15.0%)
 UniProtKB/TrEMBL accessions     19365 (83.4%)
 
 
 
 Status of entries: Protein_ID's in EMBL
 ---------------------------------------
 Protein_id            22854 (98.4%)
 
 
 
 Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
 ---------------------------------------------
 Entries with CGC-approved Gene name   7303
 
 
 GeneModel correction progress WS170 -> WS171
 -----------------------------------------
 Confirmed introns not in a CDS gene model;
 
 		+---------+--------+
 		| Introns | Change |
 		+---------+--------+
 Cambridge	|     15  |     0  |
 St Louis 	|     13  |     3  |
 		+---------+--------+
 
 
 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 help@wormbase.org
 -===================================================================================-
 
 
 
 New Data:
 ---------
 C.remanei orthologs assignments are now made using the WashU preliminary gene set.
 Syntenic alignments of the genome sequence are still included in the compara download.
 
 Genome sequence updates:
 -----------------------
 none
 
 New Fixes:
 ----------
 
 
 Known Problems:
 ---------------
 
 
 Other Changes:
 --------------
 
 
 Proposed Changes / Forthcoming Data:
 -------------------------------------
 
 
 
 Model Changes:
 ------------------------------------
 none
 
 -===================================================================================-
 
 
 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 _____________