WS174

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Release Notes

 WS174 was built by Gary Williams
 ======================================================================
 
 This directory includes:
 i)   database.WS174.*.tar.gz    -   compressed data for new release
 ii)  models.wrm.WS174           -   the latest database schema (also in above database files)
 iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
 iv)  WS174-WS173.dbcomp         -   log file reporting difference from last release
 v)   wormpep174.tar.gz          -   full Wormpep distribution corresponding to WS174
 vi)   wormrna174.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
 vii)  confirmed_genes.WS174.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
 viii) cDNA2orf.WS174.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
 ix)   gene_interpolated_map_positions.WS174.gz    - Interpolated map positions for each coding/RNA gene
 x)    clone_interpolated_map_positions.WS174.gz   - Interpolated map positions for each clone
 xi)   best_blastp_hits.WS174.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.WS174.gz   - for each C. briggsae protein, lists Best blastp match to
                                      human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
 xiii) geneIDs.WS174.gz   - list of all current gene identifiers with CGC & molecular names (when known)
 xiv)  PCR_product2gene.WS174.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:
 ----------------------------
 
        	WS174       	WS173      	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 24036)
 ------------------------------------------
 Molecular_info              22345 (93%)
 Concise_description          4524 (18.8%)
 Reference                    6981 (29%)
 CGC_approved Gene name       9116 (37.9%)
 RNAi_result                 19859 (82.6%)
 Microarray_results          19140 (79.6%)
 SAGE_transcript             20044 (83.4%)
 
 
 
 
 Wormpep data set:
 ----------------------------
 
 There are 20101 CDS in autoace, 23258 when counting 3157 alternate splice forms.
 
 The 23258 sequences contain 10,212,175 base pairs in total.
 
 Modified entries              26
 Deleted entries                8
 New entries                    6
 Reappeared entries             2
 
 Net change  +0
 
 
 
 Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 -------------------------------------------------
 Confirmed              7848 (33.7%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
 Partially_confirmed   10802 (46.4%)	Some, but not all exon bases are covered by transcript evidence
 Predicted              4608 (19.8%)	No transcriptional evidence at all
 
 
 
 Status of entries: Protein Accessions
 -------------------------------------
 UniProtKB/Swiss-Prot accessions   3512 (15.1%)
 UniProtKB/TrEMBL accessions     19384 (83.3%)
 
 
 
 Status of entries: Protein_ID's in EMBL
 ---------------------------------------
 Protein_id            22869 (98.3%)
 
 
 
 Gene <-> CDS,Transcript,Pseudogene connections (cgc-approved)
 ---------------------------------------------
 Entries with CGC-approved Gene name   7476
 
 
 GeneModel correction progress WS173 -> WS174
 -----------------------------------------
 Confirmed introns not in a CDS gene model;
 
 		+---------+--------+
 		| Introns | Change |
 		+---------+--------+
 Cambridge	|    186  |     2  |
 St Louis 	|    215  |     0  |
 		+---------+--------+
 
 
 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:
 ---------
 
 The following databases were updated for BLAST:
 
 trembl release 35
 swissprot release 52
 yeast
 
 
 
 Genome sequence updates:
 -----------------------
 
 None.
 
 New Fixes:
 ----------
 
 None.
 
 Known Problems:
 ---------------
 
 
 Other Changes:
 --------------
 
 Many Poly-A tails were masked in EST and mRNA sequences.  New Poly-A
 Site and Poly-A Signal sequence Features were defined based on the
 alignment of these sequences to the genome:
 
 - 3530 new (1931 site, 1599 signal sequence) Features were defined.
 
 - 641 old Poly-A Features (490 site, 151 signal) with no supporting
   Sequence evidence were removed (changed to Method="history").
 
 
 
 
 Proposed Changes / Forthcoming Data:
 -------------------------------------
 
 We are working with the authors of this paper:
 
 Ruby J et al. Cell. 2006 Dec 15;127(6):1193-207.  "Large-scale
 sequencing reveals 21U-RNAs and additional microRNAs and endogenous
 siRNAs in C. elegans."
 
 http://www.wormbase.org/db/misc/paper?name=WBPaper00028915;class=Paper
 
 to refine and annotate circa 4500 new elegans RNA genes.
 
 <A third class of nematode small RNAs, called 21U-RNAs, was
 discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a
 uridine 5''-monophosphate but are diverse in their remaining 20
 nucleotides, and appear modified at their 3''-terminal
 ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed
 in two broad regions of chromosome IV-primarily between protein-coding
 genes or within their introns. These loci share a large upstream motif
 that enables accurate prediction of additional 21U-RNAs. The motif is
 conserved in other nematodes, presumably because of its importance for
 producing these diverse, autonomously expressed, small RNAs
 (dasRNAs).>
 
 
 Forthcoming model changes:
 
 Added tags to ?Person and ?Paper to enable recording of negative
 connections ie Mr X did NOT contribue to this paper.
 
 Added Map_evidence to ?Transgene so that the paper that mapping data
 is taken from can be attributed
 
 Added a tags to ?Expr_pattern and ?Expression_cluster to handle
 Localizome data Note: ?Interaction class update already committed
 
 
 Model Changes:
 ------------------------------------
 
 Added DB_info line to ?Gene
 
 Replaced ?Y2H with a more generic ?YH class which contains Y2H and Y1H
 data.
 
 Added Anatomy_function class to allow the connection between
 ?Anatomy_term, ?Phenotype (proxy of biological function), and ?Gene
 and still give some information about the experiment itself. Name
 shall be "WBbtf0001"
 
 
 -===================================================================================-
 
 
 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.