Difference between revisions of "Cosmids/YACs"
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==Vector Sequences== | ==Vector Sequences== | ||
− | + | {| border="1" class="wikitable" | |
+ | | bgcolor="gray" | Clone series || Vector Sequence || Comment || Vector publication || 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] | ||
+ | |} | ||
− | + | [http://www.ncbi.nlm.nih.gov/nuccore/401849 pYAC4] [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=67379&Template=vectors Ordering] | |
+ | [[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 later the Genome Sequencing Project. | ||
− | + | <br> | |
− | |||
− | <br> | ||
==Clone ends within wormbase== | ==Clone ends within wormbase== |
Revision as of 08:29, 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.
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.
Vector Sequences
[Additional information on libraries/Methods/Protocols etc. used when generating the Physical Map of C. elegans and later the Genome Sequencing Project.
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: