Cosmid and YAC Info.
******** Warning ********
This resource is being transferred to geneservice and is temporarily unavailable
Please send all requests for C.elegans genomic clones to Audrey Fraser (firstname.lastname@example.org)
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.
- 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.
- Clone ends within wormbase
The set of clone ends is dumped as part of the gff files:
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).
C. elegans Clones.
- There are seven different types of "Clone" objects in WormBase:
|Cosmid||A*, B*, C*, D*, F*,J*,K*,M*,R*,T*,W*,Z*|
|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.