Difference between revisions of "Cosmids/YACs"
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− | == <span style="color: rgb(128, 0, 0);">Cosmid and YAC Info. </span><br> == | + | __TOC__ |
+ | <center> | ||
+ | == <span style="color: rgb(128, 0, 0);"><i>C. elegans</i> Cosmid and YAC Info. </span><br> == | ||
+ | </center><u> | ||
+ | ===Ordering=== | ||
+ | </u> | ||
+ | Please submit all requests for C.elegans genomic clones via this request portal. | ||
+ | <br> | ||
− | + | [[File:new_clone_requests_new.png|link=https://www.sanger.ac.uk/tool/c-elegans-and-pombes-clones|Clone Requests]] | |
− | |||
− | + | <u> | |
− | + | ===Nomenclature=== | |
+ | </u> | ||
+ | There are seven different types of "Clone" objects in WormBase: | ||
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|- | |- | ||
− | | Type | + | | bgcolor="gray" | Type |
− | | Nomenclature | + | | bgcolor="gray" | Nomenclature |
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| Cosmid | | Cosmid | ||
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− | + | Most Cosmids, Fosmids, YACs can be requested from Sanger via the form at the top of the page, | |
+ | |||
+ | cDNA (yk*) from Dr. Yuji Kohara. | ||
+ | |||
+ | The EGAP* plasmids can be obtained from........ | ||
+ | |||
+ | WRM [http://wiki.wormbase.org/index.php/Fosmids Vancouver_fosmid] | ||
+ | |||
+ | '''The V* plasmids are no longer available.''' | ||
+ | |||
+ | '''The EC* ESTs were distributesd by Exelixis but are no longer available.''' | ||
+ | |||
+ | <br> | ||
+ | <br> | ||
+ | <br><u> | ||
+ | |||
+ | ===Vector Sequences=== | ||
+ | </u> | ||
+ | {| border="1" class="wikitable" | ||
+ | | 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] | ||
+ | |- | ||
+ | | ZL || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lambda.seq Lambda 2001?] || <i>Sau</i>3A1 partial, probe selected || [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] | ||
+ | |- | ||
+ | | YSL || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lambda.seq Lambda 2001?] || <i>Sau</i>3A1 partial, YAC subclones || [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] | ||
+ | |- | ||
+ | | B || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | C || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Sau</i>3A1 partial, microtitre array || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | D || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Sau</i>3A1 partial, filter gridded || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | E || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Sau</i>3A1 partial, <i>Eco</i>K- host || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | R || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Eco</i>R1 partial || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | M || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Mbo</i>1 partial || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | ZC || | [ftp://ftp.sanger.ac.uk/pub/vector_sequences/pjb8.seq pJB8] || <i>Eco</i>R1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed?term=burke%20ish%20horowicz%201981&cmd=correctspelling Nucleic Acids Res. 1981 Jul 10;9(13):2989-98.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98612 X98612] | ||
+ | |- | ||
+ | | K || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/loristB.seq loristB] || <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed/3552884 Gene. 1986;49(1):9-22.] || [http://www.ncbi.nlm.nih.gov/nuccore/3319652 X98613] | ||
+ | |- | ||
+ | | T || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial || [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] | ||
+ | |- | ||
+ | | W || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Not</i>I complete, <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | F 1-28 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist2.seq lorist2] || <i>Sau</i>3A1 partial || [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] | ||
+ | |- | ||
+ | | F 29 on || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 15-56 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 57-130 || [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] | ||
+ | |- | ||
+ | | ZK131-164 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 165-177 || [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 178-192 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 193-344 || [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 345-354 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 355-514 || [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 515-552 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | 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 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 627-692 || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | ZK 693-756 || [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 757 on || [ftp://ftp.sanger.ac.uk/pub/vector_sequences/lorist6.seq lorist6] || <i>Sau</i>3A1 partial, probe selected || [http://www.ncbi.nlm.nih.gov/pubmed/3038694 Gene. 1987;53(2-3):283-6.] || [http://www.ncbi.nlm.nih.gov/nuccore/X98450.1 X98450] | ||
+ | |- | ||
+ | | 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] | ||
+ | |} | ||
+ | <br> | ||
+ | <br> | ||
+ | <br><u> | ||
+ | |||
+ | === 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><u> | ||
+ | === YAC clone Information === | ||
+ | </u> | ||
+ | Specific YAC information can be found in these publications: | ||
+ | |||
+ | [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><u> | ||
+ | ===Clone ends within wormbase=== | ||
+ | </u> | ||
+ | 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> | ||
+ | <br> | ||
+ | <br> | ||
+ | |||
− | |||
− | + | [[Category:User Guide]] |
Latest revision as of 16:21, 5 January 2021
Contents
C. elegans Cosmid and YAC Info.
Ordering
Please submit all requests for C.elegans genomic clones via this request portal.
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 via the form at the top of the page,
cDNA (yk*) from Dr. Yuji Kohara.
The EGAP* plasmids can be obtained from........
WRM Vancouver_fosmid
The V* plasmids are no longer available.
The EC* ESTs were distributesd by Exelixis but 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).