From EcoliWiki
Jump to: navigation, search

You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.

See Help:Bioinformatics Tools for more information about tools in EcoliWiki.

Short Description

Share your knowledge and ideas. How you can help. See Help pages if you need help with using the wiki
PlasMapper[1] is a web-based tool that generates graphic plasmid maps. PlasMapper needs only the sequence of the plasmid to generate a map with commonly used plasmid features such as drug resistances, promoters, terminators, restriction sites etc. PlasMapper's feature database recognizes 336 different features.

Plasmapper is available through the web, and source code is also available.


Links to sites that run the software or where it can be obtained


Hardware/Software requirements, if applicable

User notes

How to use Plasmapper

Plasmapper is fairly intuitive for a beginner but in order to maintain consistency on ecoliwiki we have provided a short How To. For detailed description on all Plasmapper features please visit Plasmappers Help Page.
Plasmapper is only able to generates and annotate plasmid maps from FASTA format sequences only, but have the choice between uploading your own file, choosing from a suppliers library or pasting FASTA sequence in text box provided. If you choose to paste FASTA sequence in text box provided it is not necessary to strip the sequence data of its single-line description header or any reference numbering, you can actually add this via (Re)generate button.
Now you can customize what features are expressed on your plasmid map that was based of the sequence. The only real thing we ask here is that under Plasmid Map Graphic Display Options in title box you put the plasmid name and define an image size that will display all plasmid features. You will know the image is not large enough because when the map is generated there will be a warning on the lower left hand size of the image telling you not all attributes are displayed, this is when you go back to Plasmid Map Graphic Display Options and choose a larger size.
Now that you have your map image generated its time to upload the image to ecoliwiki in order to add it to your desired ecoliwiki page. Instructions can be found under Help:Images.

See Also


See Help:References for how to manage references in EcoliWiki.

  1. Dong, X et al. (2004) PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res. 32 W660-4 PubMed