Difference between revisions of "Cosmids/YACs"
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− | < | + | |
− | + | ==Nomenclature== | |
− | < | + | |
− | <br> | + | 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*<br> | ||
+ | |- | ||
+ | | YAC | ||
+ | | Y* | ||
+ | |- | ||
+ | | cDNA | ||
+ | | yk*, EC*, EB*, OST*, CK*, EF*, CEE*, CEM*, CES*, CB*, CN*, cm*<br> | ||
+ | |- | ||
+ | | Plasmid: PCR clones | ||
+ | | V*,EGAP* | ||
+ | |- | ||
+ | | Other | ||
+ | | telo clones, 1 BAC, plasmid<br> | ||
+ | |} | ||
+ | |||
+ | 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.''' | ||
+ | |||
==Vector Sequences== | ==Vector Sequences== | ||
{| border="1" class="wikitable" | {| border="1" class="wikitable" | ||
− | | bgcolor="gray" | Clone series || Vector Sequence || Comment || Vector publication || NCBI/DB Accession | + | | bgcolor="gray" | Clone series || bgcolor="gray" | Vector Sequence || bgcolor="gray" | Comment || bgcolor="gray" | Vector publication || bgcolor="gray" | NCBI/DB Accession |
|- | |- | ||
| A || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lambda.seq Lambda 2001?] || <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed/6099311 Gene. 1984 Dec;32(1-2):217-24.] || [http://genome-www.stanford.edu/vectordb/vector_descrip/NOTCOMPL/LAM2001.SEQ.html Vector db] | | A || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lambda.seq Lambda 2001?] || <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed/6099311 Gene. 1984 Dec;32(1-2):217-24.] || [http://genome-www.stanford.edu/vectordb/vector_descrip/NOTCOMPL/LAM2001.SEQ.html Vector db] | ||
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− | + | == Protocols and Methods == | |
− | [[http://books.google.co.uk/books?id=AUxd_e4mzHIC&pg=PA538&lpg=PA538&dq=pJB8&source=bl&ots=ViMao3y2x3&sig=QXZxjqVNC6u99qDsOEloaN-i1Us&hl=en&ei=HbxFTIfMOIPO4gaim8T7CQ&sa=X&oi=book_result&ct=result&resnum=9&ved=0CDIQ6AEwCA#v=onepage&q=pJB8&f=false Additional information] on libraries/Methods/Protocols etc. used when generating the Physical Map of C. elegans and | + | [[http://books.google.co.uk/books?id=AUxd_e4mzHIC&pg=PA538&lpg=PA538&dq=pJB8&source=bl&ots=ViMao3y2x3&sig=QXZxjqVNC6u99qDsOEloaN-i1Us&hl=en&ei=HbxFTIfMOIPO4gaim8T7CQ&sa=X&oi=book_result&ct=result&resnum=9&ved=0CDIQ6AEwCA#v=onepage&q=pJB8&f=false Additional information] on libraries/Methods/Protocols etc. used when generating the Physical Map of C. elegans and the Genome Sequencing Project. |
<br> | <br> | ||
− | == | + | == YAC clone Information == |
− | + | Specific YAC information can be found in these publications: | |
− | [http://www. | + | [http://www.nature.com/doifinder/10.1038/335184a0 Nature. 1988 Sep 8;335(6186):184-6. Genome linking with yeast artificial chromosomes. Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y.] |
− | + | [http://www.sciencemag.org/cgi/content/abstract/236/4803/806 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] | |
− | + | <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> | ||
− | <br> | + | <center> |
+ | http://wormbase.sanger.ac.uk/wiki_pics/yac.png | ||
+ | </center> | ||
+ | <br> | ||
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− | + | ==Clone ends within wormbase== | |
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− | + | 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 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). | |
− | + | <br> | |
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Revision as of 08:40, 21 July 2010
Contents
C. elegans Cosmid and YAC Info.
Ordering
Please submit all requests for C.elegans genomic clones via this request form.
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.
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.
Vector Sequences
Protocols and Methods
[Additional information on libraries/Methods/Protocols etc. used when generating the Physical Map of C. elegans and the Genome Sequencing Project.
YAC clone Information
Specific YAC information can be found in these publications:
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.
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).