Vectors
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
Yeast
Plant
CAMBIA Plant Transformation Vectors
