Vectors: Difference between revisions

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==General information==
==General information==


===Stringent vs. relaxed replication===
===Online vector databases===
Plasmid replication control is usually controlled by balancing the levels of a positive and a negative regulator of replication.  For some plasmids (pMB1/colE1 replicons) the positive regulator is an RNA and in others (e.g. pSC101) it is a protein.  Plasmids with a protein positive regulator will not replicate in the abscence of protein production - ''stringent control'' (although not the same as the stringent response due to a shortage of loaded tRNAs).  Plasmids with an RNA positive regulator will continue to replicate in the  abscence of protein production.  This is termed ''relaxed control''.  High yields of plasmid may be obtained by halting protein production (via chloroamphenicol) when the culture reaches a high density and then continuing incubation for a number of hours.  This might be of practical relevance when prepping the 1 and 3 series of Synthetic Biology plasmids.--[[User:Bcanton|BC]] 19:05, 3 Sep 2005 (EDT)
 
===Online Vector Databases===
You can often find vector information at [http://www.ncbi.nlm.nih.gov/ NCBI,] either directly or in their list of vectors screened for contamination of new sequence at [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html Vecscreen].  
You can often find vector information at [http://www.ncbi.nlm.nih.gov/ NCBI,] either directly or in their list of vectors screened for contamination of new sequence at [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html Vecscreen].  


[http://seq.yeastgenome.org/vectordb/ VectorDB] contains information about many common vectors, including yeast vectors.
[http://seq.yeastgenome.org/vectordb/ VectorDB] contains information about many common vectors, including yeast vectors.


[http://www.embl-hamburg.de/display?file=~geerlof/webPP/vectordb/vector_index.html EMBL] maintains a large database of vectors.
[http://www.embl-hamburg.de/services/protein/vectors_strains/vectors.html The EMBL Hamburg outstation] maintains a large database of vectors.
 
[http://image.llnl.gov/image/html/vectors.shtml I.M.A.G.E. Consortium Vectors] contains information about plasmids commonly used in EST collections such as those sold by [http://www.openbiosystems.com OpenBioSystems] and [http://www.invitrogen.com Invitrogen].


For eukaryotic vectors (Fish, Xenopus) see [http://beckmancenter.ahc.umn.edu/cgi-bin/plasmidlookup.pl Minnesota].
For eukaryotic vectors (Fish, Xenopus) see [http://beckmancenter.ahc.umn.edu/cgi-bin/plasmidlookup.pl Minnesota].
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[http://www.epibio.com/sequences.asp Epicentre] also maintains its own list.
[http://www.epibio.com/sequences.asp Epicentre] also maintains its own list.
[http://www.lucigen.com/catalog/index.php?cPath=14_15 Lucigen] provides transcription-free vectors for cloning AT-rich and other difficult DNAs.


[http://www.addgene.org/vectors Addgene's Vector DB] contains most of the information from Stanford's VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts.  (However, it seems to be rather sparse when it comes to ''Escherichia coli'' vectors.)  Note that [http://www.addgene.org Addgene] is a a non-profit plasmid repository where scientists can archive and share their plasmids.  They encourage and invite labs to deposit plasmids at Addgene. They help you with data submission and all tech transfer issues.  Plasmids can be requested from Addgene for a fee to cover expenses.
[http://www.addgene.org/vectors Addgene's Vector DB] contains most of the information from Stanford's VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts.  (However, it seems to be rather sparse when it comes to ''Escherichia coli'' vectors.)  Note that [http://www.addgene.org Addgene] is a a non-profit plasmid repository where scientists can archive and share their plasmids.  They encourage and invite labs to deposit plasmids at Addgene. They help you with data submission and all tech transfer issues.  Plasmids can be requested from Addgene for a fee to cover expenses.
[http://bioinfoman.com/bm/pcs.php Bioinfoman] also has a 5000+ long list of vector sequences.
[http://plasmid.med.harvard.edu/PLASMID/ PlasmID] is an online database and DNA repository maintained for  plasmids, including [http://plasmid.med.harvard.edu/PLASMID/GetAllVectors.do empty vectors] useful for a variety of techniques, and open reading frame (ORF) clones relevant to human, yeast, and several bacterial pathogens. All clones can be requested individually, and ORF clones can also be viewed and requested as grouped [http://plasmid.med.harvard.edu/PLASMID/GetCollectionList.do collections]. PlasmID is maintained by the [http://dnaseq.med.harvard.edu DF/HCC DNA Resource Core] at the Harvard Institute of Proteomics, Harvard Medical School.


===Annotation===
===Annotation===
[http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper]: "automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format."  It can also output GenBank format.  Reference: Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart "PlasMapper: a web server for drawing and auto-annotating plasmid maps" Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.
[http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper]: "automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format."  It can also output GenBank format.  Reference: Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart "PlasMapper: a web server for drawing and auto-annotating plasmid maps" Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.
*One drawback to this tool is that although it finds ORFs, it doesn't necessarily identify them. --[[Reshma Shetty | RS]]
*One drawback to this tool is that although it finds ORFs, it doesn't necessarily identify them. --[[Reshma Shetty | RS]]
*A very nice aspect of PlasMapper is that it identifies features of a sequence and puts them into GenBank format - very handy to prepare sequences for submission to GenBank. --[[User:Rgodiska]]
Also check out [http://www.biology.utah.edu/jorgensen/wayned/ape/ APe], A Plasmid Editor.
Also check out [http://www.biology.utah.edu/jorgensen/wayned/ape/ APe], A Plasmid Editor.
*Has some built-in features for annotation (a few genes, many restriction enzymes).  Allows you to make custom "feature libraries" for annotating sequences
*Can edit features found, unlike Plasmapper --[[User:Melissali|mel]] 18:50, 12 June 2007 (EDT)


==''Escherichia coli''==
==''Escherichia coli''==


===Information===
See [[Escherichia coli/Vectors]].


*[[Bacterial artificial chromosomes]]
==Yeast==
*[[Synthetic Biology:Vectors | Synthetic Biology vectors]]


===Replicon Compatibility===
[[Yeast_vectors|Nomenclature and types]]
''The following are groups of replicons that '''can''' be used with the bold replicon in the one cell''.
*'''colE1''' - p15A,R6K, and F
*'''pMB1''' - p15A,R6K, and F
*??


Some sets of vectors with compatible origins are available as a part of the  [http://www.emdbiosciences.com/html/NVG/DuetTable.html Novagen Duet system]. (from [[User:Tk | TK]])
[[Yeast artificial chromosomes]]


===Individual vector links===
==Plant==
''Note: searching for cloning vector <insert vector name> when looking for vector sequences in NCBI Entrez Nucleotide search. It helps to cut down on the number of hits.''
[http://www.cambia.org/daisy/cambia/lab/materials.html CAMBIA Plant Transformation Vectors]


*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=6691170 pUC19]
[http://www.psb.ugent.be/gateway/index.php Gateway compatible binary plant vectors]
*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=1817728 pBeloBAC11]
*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=4878025 pBACe3.6]
*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=9507713 F plasmid]
*pSCANS [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Retrieve&list_uids=6689911&dopt=GenBank genbank] [http://genome.bnl.gov/Vectors/pscans.php vector info] [http://www.genome.bnl.gov/Protocols/pscans.shtml cookbook]
*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=42704 pSC101 replication origin]


===Other references===
==Other==
*[http://www.emdbiosciences.com/g.asp?f=NVG/pETtable.html Novagen pET vector table]
See [[Gateway cloning system]].
**table with links to properties/sequences of pET vectors
**note: slow to load


==Yeast==
[[Category:DNA]]
 
[[Yeast_vectors|Nomenclature and types]]

Revision as of 16:16, 28 December 2008

This page contains various information relating to vectors used in OpenWetWare labs.

General information

Online vector databases

You can often find vector information at NCBI, either directly or in their list of vectors screened for contamination of new sequence at Vecscreen.

VectorDB contains information about many common vectors, including yeast vectors.

The EMBL Hamburg outstation maintains a large database of vectors.

I.M.A.G.E. Consortium Vectors contains information about plasmids commonly used in EST collections such as those sold by OpenBioSystems and Invitrogen.

For eukaryotic vectors (Fish, Xenopus) see Minnesota.

The Forsburg Lab maintains a list of Fisson Yeast vectors.

Promega maintains a list of their vectors.

NEB maintains a list of common vectors.

Epicentre also maintains its own list.

Lucigen provides transcription-free vectors for cloning AT-rich and other difficult DNAs.

Addgene's Vector DB contains most of the information from Stanford's VectorDB, plus more vector information they have curated from commercial websites and added through our plasmid curation efforts. (However, it seems to be rather sparse when it comes to Escherichia coli vectors.) Note that Addgene is a a non-profit plasmid repository where scientists can archive and share their plasmids. They encourage and invite labs to deposit plasmids at Addgene. They help you with data submission and all tech transfer issues. Plasmids can be requested from Addgene for a fee to cover expenses.

Bioinfoman also has a 5000+ long list of vector sequences.

PlasmID is an online database and DNA repository maintained for plasmids, including empty vectors useful for a variety of techniques, and open reading frame (ORF) clones relevant to human, yeast, and several bacterial pathogens. All clones can be requested individually, and ORF clones can also be viewed and requested as grouped collections. PlasmID is maintained by the DF/HCC DNA Resource Core at the Harvard Institute of Proteomics, Harvard Medical School.

Annotation

PlasMapper: "automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format." It can also output GenBank format. Reference: Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart "PlasMapper: a web server for drawing and auto-annotating plasmid maps" Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4.

  • One drawback to this tool is that although it finds ORFs, it doesn't necessarily identify them. -- RS
  • A very nice aspect of PlasMapper is that it identifies features of a sequence and puts them into GenBank format - very handy to prepare sequences for submission to GenBank. --User:Rgodiska

Also check out APe, A Plasmid Editor.

  • Has some built-in features for annotation (a few genes, many restriction enzymes). Allows you to make custom "feature libraries" for annotating sequences
  • Can edit features found, unlike Plasmapper --mel 18:50, 12 June 2007 (EDT)

Escherichia coli

See Escherichia coli/Vectors.

Yeast

Nomenclature and types

Yeast artificial chromosomes

Plant

CAMBIA Plant Transformation Vectors

Gateway compatible binary plant vectors

Other

See Gateway cloning system.

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