Difference between revisions of "WS196"

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New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008
+
<pre>New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008
  
  
 
WS196 was built by Mary Ann and Anthony
 
WS196 was built by Mary Ann and Anthony
==========================================================
+
======================================================================
  
This directory includes: i) database.WS196.*.tar.gz - compressed data for new release ii) models.wrm.WS196 - the latest database schema (also in above database files) iii) CHROMOSOMES/subdir - contains 3 files (DNA, GFF & AGP per chromosome) iv) WS196-WS195.dbcomp - log file reporting difference from last release v) wormpep196.tar.gz - full Wormpep distribution corresponding to WS196 vi) wormrna196.tar.gz - latest WormRNA release containing non-coding RNA's in the genome vii) confirmed_genes.WS196.gz - DNA sequences of all genes confirmed by EST &/or cDNA viii) cDNA2orf.WS196.gz - Latest set of ORF connections to each cDNA (EST, OST, mRNA) ix) gene_interpolated_map_positions.WS196.gz - Interpolated map positions for each coding/RNA gene x) clone_interpolated_map_positions.WS196.gz - Interpolated map positions for each clone xi) best_blastp_hits.WS196.gz - for each C. elegans WormPep protein, lists Best blastp match to
+
This directory includes:
 
+
i)   database.WS196.*.tar.gz   -   compressed data for new release
                          human, fly, yeast, C. briggsae, and SwissProt & TrEMBL proteins.
+
ii) models.wrm.WS196           -   the latest database schema (also in above database files)
 
+
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
xii) best_blastp_hits_brigprot.WS196.gz - for each C. briggsae protein, lists Best blastp match to
+
iv) WS196-WS195.dbcomp         -   log file reporting difference from last release
 
+
v)   wormpep196.tar.gz         -   full Wormpep distribution corresponding to WS196
                                    human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
+
vi)   wormrna196.tar.gz         -   latest WormRNA release containing non-coding RNA's in the genome
 
+
vii) confirmed_genes.WS196.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
xiii) geneIDs.WS196.gz - list of all current gene identifiers with CGC & molecular names (when known) xiv) PCR_product2gene.WS196.gz - Mappings between PCR products and overlapping Genes
+
viii) cDNA2orf.WS196.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
 +
ix)   gene_interpolated_map_positions.WS196.gz   - Interpolated map positions for each coding/RNA gene
 +
x)   clone_interpolated_map_positions.WS196.gz   - Interpolated map positions for each clone
 +
xi)   best_blastp_hits.WS196.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.WS196.gz   - for each C. briggsae protein, lists Best blastp match to
 +
                                    human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
 +
xiii) geneIDs.WS196.gz   - list of all current gene identifiers with CGC & molecular names (when known)
 +
xiv) PCR_product2gene.WS196.gz   - Mappings between PCR products and overlapping Genes
  
  
 
Release notes on the web:
 
Release notes on the web:
 +
-------------------------
 +
http://www.wormbase.org/wiki/index.php/Release_Schedule
  
http://www.wormbase.org/wiki/index.php/Release_Schedule
 
  
  
 
Genome sequence composition:
 
Genome sequence composition:
 +
----------------------------
  
      WS196      WS195      change
+
      WS196      WS195      change
 
+
----------------------------------------------
a 32365950 32365950 +0 c 17779889 17779889 +0 g 17756041 17756041 +0 t 32365753 32365753 +0 n 0 0 +0 - 0 0 +0
+
a   32365950 32365950   +0
 +
c   17779889 17779889   +0
 +
g   17756041 17756041   +0
 +
t   32365753 32365753   +0
 +
n   0       0         +0
 +
-   0       0         +0
  
Total 100267633 100267633 +0
+
Total 100267633 100267633   +0
  
  
 
Chromosomal Changes:
 
Chromosomal Changes:
 
+
--------------------
 
There are no changes to the chromosome sequences in this release.
 
There are no changes to the chromosome sequences in this release.
  
  
 
Gene data set (Live C.elegans genes 29872)
 
Gene data set (Live C.elegans genes 29872)
 +
------------------------------------------
 +
Molecular_info              28155 (94.3%)
 +
Concise_description        5447 (18.2%)
 +
Reference                  13254 (44.4%)
 +
WormBase_approved Gene name 15636 (52.3%)
 +
RNAi_result                20799 (69.6%)
 +
Microarray_results          20438 (68.4%)
 +
SAGE_transcript            18838 (63.1%)
  
Molecular_info 28155 (94.3%) Concise_description 5447 (18.2%) Reference 13254 (44.4%) WormBase_approved Gene name 15636 (52.3%) RNAi_result 20799 (69.6%) Microarray_results 20438 (68.4%) SAGE_transcript 18838 (63.1%)
 
  
  
  
 
Wormpep data set:
 
Wormpep data set:
 +
----------------------------
  
 
There are 20191 CDS in autoace, 23902 when counting 3711 alternate splice forms.
 
There are 20191 CDS in autoace, 23902 when counting 3711 alternate splice forms.
Line 47: Line 70:
 
The 23902 sequences contain 10,518,004 base pairs in total.
 
The 23902 sequences contain 10,518,004 base pairs in total.
  
Modified entries 66 Deleted entries 25 New entries 21 Reappeared entries 0
+
Modified entries     66
 +
Deleted entries       25
 +
New entries           21
 +
Reappeared entries   0
 +
 
 +
Net change  -4
  
Net change -4
 
  
  
 
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 
Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
 +
-------------------------------------------------
 +
Confirmed              8517 (35.6%) Every base of every exon has transcription evidence (mRNA, EST etc.)
 +
Partially_confirmed  10985 (46.0%) Some, but not all exon bases are covered by transcript evidence
 +
Predicted              4400 (18.4%) No transcriptional evidence at all
  
Confirmed 8517 (35.6%) Every base of every exon has transcription evidence (mRNA, EST etc.) Partially_confirmed 10985 (46.0%) Some, but not all exon bases are covered by transcript evidence Predicted 4400 (18.4%) No transcriptional evidence at all
 
  
  
 
Status of entries: Protein Accessions
 
Status of entries: Protein Accessions
 +
-------------------------------------
 +
UniProtKB accessions  23768 (99.4%)
  
UniProtKB accessions 23768 (99.4%)
 
  
  
 
Status of entries: Protein_ID's in EMBL
 
Status of entries: Protein_ID's in EMBL
 +
---------------------------------------
 +
Protein_id            23772 (99.5%)
  
Protein_id 23772 (99.5%)
 
  
  
 
Gene <-> CDS,Transcript,Pseudogene connections
 
Gene <-> CDS,Transcript,Pseudogene connections
 
+
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name 13967
+
Caenorhabditis elegans entries with WormBase-approved Gene name 13967
  
  
 
GeneModel correction progress WS195 -> WS196
 
GeneModel correction progress WS195 -> WS196
 
+
-----------------------------------------
 
Confirmed introns not in a CDS gene model;
 
Confirmed introns not in a CDS gene model;
  
+---------+--------+ | Introns | Change | +---------+--------+ Cambridge | 40 | 13 | St Louis | 118 | 15 | +---------+--------+
+
+---------+--------+
 +
| Introns | Change |
 +
+---------+--------+
 +
Cambridge |     40 |   13 |
 +
St Louis |   118 |   15 |
 +
+---------+--------+
  
  
 
Members of known repeat families that overlap predicted exons;
 
Members of known repeat families that overlap predicted exons;
  
+---------+--------+ | Repeats | Change | +---------+--------+ Cambridge | 6 | 0 | St Louis | 6 | 0 | +---------+--------+
+
+---------+--------+
 +
| Repeats | Change |
 +
+---------+--------+
 +
Cambridge |     6 |     0 |
 +
St Louis |     6 |     0 |
 +
+---------+--------+
 +
 
  
  
 
Synchronisation with GenBank / EMBL:
 
Synchronisation with GenBank / EMBL:
 +
------------------------------------
  
 
No synchronisation issues
 
No synchronisation issues
Line 90: Line 134:
  
 
There are no gaps remaining in the genome sequence
 
There are no gaps remaining in the genome sequence
 +
---------------
 +
For more info mail help@wormbase.org
 +
-===================================================================================-
  
For more info mail worm@sanger.ac.uk -===================================================================================-
 
  
  
 
New Data:
 
New Data:
 
+
---------
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.
+
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.
  
 
There has been some manual correction of the C. briggsae nGASP gene predictions.
 
There has been some manual correction of the C. briggsae nGASP gene predictions.
  
Precalculated protein alignments are now made for each main WormBase species. This is available on the Sanger FTP site ftp.sanger.ac.uk/pub2/wormbase/live_release/wormpep_clw.sql.bz2 . For info contact WormBase.
+
Precalculated protein alignments are now made for each main WormBase species.
 +
This is available on the Sanger FTP site ftp.sanger.ac.uk/pub2/wormbase/live_release/wormpep_clw.sql.bz2 . For info contact WormBase.
  
 
Genome sequence updates:
 
Genome sequence updates:
 +
-----------------------
  
  
 
New Fixes:
 
New Fixes:
 +
----------
  
  
 
Known Problems:
 
Known Problems:
 
+
---------------
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. They are still available in the GFF files and so visible in the genome browser but not via querying the acedb database.
+
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.
 +
They are still available in the GFF files and so visible in the genome browser but not via querying the acedb database.  
  
  
 
Other Changes:
 
Other Changes:
 +
--------------
  
 
Proposed Changes / Forthcoming Data:
 
Proposed Changes / Forthcoming Data:
 +
-------------------------------------
 +
  
  
 
Model Changes:
 
Model Changes:
 
+
------------------------------------
 
added Person to #Affiliation
 
added Person to #Affiliation
  
Line 127: Line 180:
  
 
Quick installation guide for UNIX/Linux systems
 
Quick installation guide for UNIX/Linux systems
 +
-----------------------------------------------
  
1. Create a new directory to contain your copy of WormBase, e.g. /users/yourname/wormbase
+
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.
+
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).
+
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.
+
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.
+
5. See the acedb website for more information about acedb and
 +
using xace.
  
____________ END _____________
+
____________ END _____________
 +
</pre>

Latest revision as of 16:41, 21 December 2011

New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008


WS196 was built by Mary Ann and Anthony
======================================================================

This directory includes:
i)   database.WS196.*.tar.gz    -   compressed data for new release
ii)  models.wrm.WS196           -   the latest database schema (also in above database files)
iii) CHROMOSOMES/subdir         -   contains 3 files (DNA, GFF & AGP per chromosome)
iv)  WS196-WS195.dbcomp         -   log file reporting difference from last release
v)   wormpep196.tar.gz          -   full Wormpep distribution corresponding to WS196
vi)   wormrna196.tar.gz          -   latest WormRNA release containing non-coding RNA's in the genome
vii)  confirmed_genes.WS196.gz   -   DNA sequences of all genes confirmed by EST &/or cDNA
viii) cDNA2orf.WS196.gz           -   Latest set of ORF connections to each cDNA (EST, OST, mRNA)
ix)   gene_interpolated_map_positions.WS196.gz    - Interpolated map positions for each coding/RNA gene
x)    clone_interpolated_map_positions.WS196.gz   - Interpolated map positions for each clone
xi)   best_blastp_hits.WS196.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.WS196.gz   - for each C. briggsae protein, lists Best blastp match to
                                     human, fly, yeast, C. elegans, and SwissProt & TrEMBL proteins.
xiii) geneIDs.WS196.gz   - list of all current gene identifiers with CGC & molecular names (when known)
xiv)  PCR_product2gene.WS196.gz   - Mappings between PCR products and overlapping Genes


Release notes on the web:
-------------------------
http://www.wormbase.org/wiki/index.php/Release_Schedule



Genome sequence composition:
----------------------------

       	WS196       	WS195      	change
----------------------------------------------
a    	32365950	32365950	  +0
c    	17779889	17779889	  +0
g    	17756041	17756041	  +0
t    	32365753	32365753	  +0
n    	0       	0       	  +0
-    	0       	0       	  +0

Total	100267633	100267633	  +0


Chromosomal Changes:
--------------------
There are no changes to the chromosome sequences in this release.


Gene data set (Live C.elegans genes 29872)
------------------------------------------
Molecular_info              28155 (94.3%)
Concise_description         5447 (18.2%)
Reference                   13254 (44.4%)
WormBase_approved Gene name 15636 (52.3%)
RNAi_result                 20799 (69.6%)
Microarray_results          20438 (68.4%)
SAGE_transcript             18838 (63.1%)




Wormpep data set:
----------------------------

There are 20191 CDS in autoace, 23902 when counting 3711 alternate splice forms.

The 23902 sequences contain 10,518,004 base pairs in total.

Modified entries      66
Deleted entries       25
New entries           21
Reappeared entries    0

Net change  -4



Status of entries: Confidence level of prediction (based on the amount of transcript evidence)
-------------------------------------------------
Confirmed              8517 (35.6%)	Every base of every exon has transcription evidence (mRNA, EST etc.)
Partially_confirmed   10985 (46.0%)	Some, but not all exon bases are covered by transcript evidence
Predicted              4400 (18.4%)	No transcriptional evidence at all



Status of entries: Protein Accessions
-------------------------------------
UniProtKB accessions  23768 (99.4%)



Status of entries: Protein_ID's in EMBL
---------------------------------------
Protein_id            23772 (99.5%)



Gene <-> CDS,Transcript,Pseudogene connections
----------------------------------------------
Caenorhabditis elegans entries with WormBase-approved Gene name  13967


GeneModel correction progress WS195 -> WS196
-----------------------------------------
Confirmed introns not in a CDS gene model;

		+---------+--------+
		| Introns | Change |
		+---------+--------+
Cambridge	|     40  |    13  |
St Louis 	|    118  |    15  |
		+---------+--------+


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:
---------
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.

There has been some manual correction of the C. briggsae nGASP gene predictions.

Precalculated protein alignments are now made for each main WormBase species.
This is available on the Sanger FTP site ftp.sanger.ac.uk/pub2/wormbase/live_release/wormpep_clw.sql.bz2 . For info contact WormBase.

Genome sequence updates:
-----------------------


New Fixes:
----------


Known Problems:
---------------
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.
They are still available in the GFF files and so visible in the genome browser but not via querying the acedb database. 


Other Changes:
--------------

Proposed Changes / Forthcoming Data:
-------------------------------------



Model Changes:
------------------------------------
added Person to #Affiliation


-===================================================================================-


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 _____________