Difference between revisions of "Cosmids/YACs"
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== <span style="color: rgb(128, 0, 0);"><i>C. elegans</i> Cosmid and YAC Info. </span><br> == | == <span style="color: rgb(128, 0, 0);"><i>C. elegans</i> Cosmid and YAC Info. </span><br> == | ||
− | + | </center><u> | |
− | ==Ordering== | + | ===Ordering=== |
− | + | </u> | |
Please submit all requests for C.elegans genomic clones via this request form. | Please submit all requests for C.elegans genomic clones via this request form. | ||
− | [http://www.sanger.ac.uk/technology/clonerequests/ | + | [http://www.sanger.ac.uk/technology/clonerequests/ http://wormbase.sanger.ac.uk/wiki_pics/Clone_request_form.gif] |
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. | ||
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<br> | <br> | ||
<b><font color=red size=4>Important!</font></b><br> | <b><font color=red size=4>Important!</font></b><br> | ||
− | '''Please remember to include a [http://fedex.com/gb/account/ | + | '''Please remember to include a [http://fedex.com/gb/account/ http://wormbase.sanger.ac.uk/wiki_pics/fedex.jpeg] <b>or</b> [http://www.dhl.co.uk/publish/gb/en/eshipping/open_a_dhl_account.high.html http://wormbase.sanger.ac.uk/wiki_pics/dhl.jpeg] Account number''' to which shipping cost can be charged. |
<br> | <br> | ||
<br> | <br> | ||
− | + | <br><u> | |
− | + | ===Nomenclature=== | |
− | ==Nomenclature== | + | </u> |
− | |||
There are seven different types of "Clone" objects in WormBase: | There are seven different types of "Clone" objects in WormBase: | ||
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'''The V* plasmids are no longer available.''' | '''The V* plasmids are no longer available.''' | ||
− | + | <br> | |
− | + | <br> | |
− | ==Vector Sequences== | + | <br><u> |
− | + | ===Vector Sequences=== | |
+ | </u> | ||
{| border="1" class="wikitable" | {| border="1" class="wikitable" | ||
| bgcolor="gray" | Clone series || bgcolor="gray" | Vector Sequence || bgcolor="gray" | Comment || bgcolor="gray" | Vector publication || bgcolor="gray" | NCBI/DB Accession | | bgcolor="gray" | Clone series || bgcolor="gray" | Vector Sequence || bgcolor="gray" | Comment || bgcolor="gray" | Vector publication || bgcolor="gray" | NCBI/DB Accession | ||
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| ZK 553-596 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3301536 Gene. 1987;53(2-3):275-81.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98409.1 X98409] | | ZK 553-596 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3301536 Gene. 1987;53(2-3):275-81.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98409.1 X98409] | ||
|- | |- | ||
− | | ZK 597-616 || lorist || <i>Sau</i>3A1 partial, probe selected || | + | | ZK 597-616 || lorist || <i>Sau</i>3A1 partial, probe selected || || |
|- | |- | ||
| ZK 617-626 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3301536 Gene. 1987;53(2-3):275-81.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98409.1 X98409] | | ZK 617-626 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3301536 Gene. 1987;53(2-3):275-81.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98409.1 X98409] | ||
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|- | |- | ||
| Y || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pYAC4.seq pYAC4] || || [http://www.ncbi.nlm.nih.gov/pubmed/8163163 Gene. 1994 Apr 8;141(1):125-7.] || [http://www.ncbi.nlm.nih.gov/nuccore/401849 XXU01086] [http://genome-www.stanford.edu/vectordb/vector_descrip/PYAC4.html Vector db] | | Y || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pYAC4.seq pYAC4] || || [http://www.ncbi.nlm.nih.gov/pubmed/8163163 Gene. 1994 Apr 8;141(1):125-7.] || [http://www.ncbi.nlm.nih.gov/nuccore/401849 XXU01086] [http://genome-www.stanford.edu/vectordb/vector_descrip/PYAC4.html Vector db] | ||
− | |} | + | |}</center> |
− | + | <br> | |
− | == Protocols and Methods == | + | <br> |
− | + | <br><u> | |
− | [[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 | + | === Protocols and Methods === |
− | + | </u> | |
+ | The Protocols and methods used when generating the Physical Map of C. elegans and the Genome Sequencing Project can be found in this book chapter [[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 Methods in cell biology, Volume 48] | ||
+ | <br> | ||
<br> | <br> | ||
− | + | <br><u> | |
− | == YAC clone Information == | + | === YAC clone Information === |
− | + | </u> | |
Specific YAC information can be found in these publications: | Specific YAC information can be found in these publications: | ||
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</center> | </center> | ||
<br> | <br> | ||
− | + | <br> | |
− | + | <br><u> | |
− | + | ===Clone ends within wormbase=== | |
− | + | </u> | |
− | ==Clone ends within wormbase== | ||
− | |||
The set of clone ends is dumped as part of the gff files: | The set of clone ends is dumped as part of the gff files: | ||
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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). | 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> | |
+ | <br> | ||
<br> | <br> |
Revision as of 09:35, 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 or 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
The Protocols and methods used when generating the Physical Map of C. elegans and the Genome Sequencing Project can be found in this book chapter [Methods in cell biology, Volume 48
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).