Difference between revisions of "Cosmids/YACs"

From WormBaseWiki
Jump to navigationJump to search
Line 10: Line 10:
  
 
Details are then automatically forwarded to [mailto:archives@sanger.ac.uk Anne Angell].  Please do not send request directly to this address.
 
Details are then automatically forwarded to [mailto:archives@sanger.ac.uk Anne Angell].  Please do not send request directly to this address.
 
+
<br>
 +
<br>
 +
<b><font color=red size=4>Important!</font></b><br>
 
'''Please remember to include a [http://fedex.com/gb/account/ FedEx] / [http://www.dhl.co.uk/publish/gb/en/eshipping/open_a_dhl_account.high.html DHL] Account number''' to which shipping cost can be charged.  
 
'''Please remember to include a [http://fedex.com/gb/account/ FedEx] / [http://www.dhl.co.uk/publish/gb/en/eshipping/open_a_dhl_account.high.html DHL] Account number''' to which shipping cost can be charged.  
 +
<br>
 +
<br>
 +
<b><font color=blue size=4>Note</font></b> When ordering YAC clones.<br>
 +
Suffixes appended to YAC names (e.g. Y73B3A, Y73B3B) indicate sequenced segments of the YAC that have been used to bridge gaps between finished Cosmids<br>
 +
<br>
 +
They do not exist as subclones so you will be sent the whole YAC.<br>
  
Note that the suffixes to YAC names (e.g. Y73B3A, Y73B3B) indicate sequenced segments of the YAC (Y73B3 in this case). They do not exist as subclones. You will be sent the whole YAC.<br>  
+
<center>
 
+
http://wormbase.sanger.ac.uk/yac.png
[[File:yac.pdf]]
+
</center>
 
 
 
<br>
 
<br>
  

Revision as of 14:09, 20 July 2010

C. elegans Cosmid and YAC Info.

Ordering

Please submit all requests for C.elegans genomic clones via this request form.

Request

Details are then automatically forwarded to Anne Angell. Please do not send request directly to this address.

Important!
Please remember to include a FedEx / DHL Account number to which shipping cost can be charged.

Note When ordering YAC clones.
Suffixes appended to YAC names (e.g. Y73B3A, Y73B3B) indicate sequenced segments of the YAC that have been used to bridge gaps between finished Cosmids

They do not exist as subclones so you will be sent the whole YAC.

yac.png


Vector Sequences

If you want the actual sequence of the vectors used they are on the Sanger FTP site.

This should help you identify the vector for the clone you are interested in.


pYAC4 Ordering


Clone ends within wormbase

The set of clone ends is dumped as part of the gff files:

http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/GFF_files.shtml

This is the source for the extents displayed in WormBase.

The caveat with this is that the 'true' end is not marked up for all clones. The early cosmids do not have such annotations because nobody thought about marking them up. Later cosmids do have clone left and right ends as this became part of the standard procedure. Finally, many of the YACs do not have clone ends because the segment submitted to GenBank/EMBL is much smaller than the full clone, and hence the true ends lie within sequences already finished at that stage of the sequencing (i.e. we never went back to update clone ends in sequence already finished).


Nomenclature

There are seven different types of "Clone" objects in WormBase:


Type Nomenclature
Cosmid A*, B*, C*, D*, F*,J*,K*,M*,R*,T*,W*,Z*
Fosmid H* WRM*
YAC Y*
cDNA yk*, EC*, EB*, OST*, CK*, EF*, CEE*, CEM*, CES*, CB*, CN*, cm*
Plasmid: PCR clones V*,EGAP*
Other telo clones, 1 BAC, plasmid

Most cosmids, fosmids, YACs can be requested from Sanger, cDNA (yk*) from Dr. Yuji Kohara. The EGAP* plasmids can be obtained from MRC Geneservice.

The V* plasmids are no longer available.

References

YAC information can be found in this publication:

Nature. 1988 Sep 8;335(6186):184-6. Genome linking with yeast artificial chromosomes. Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y.

science 1987 May 15;236(806-812) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. DT Burke, GF Carle, and MV Olson