Primrose

A program for identifying potentially useful oligonucleotides for use as probes or PCR primers as phylogenetic tools.

To download Primrose click on the button below. Alternatively visit this site's download page.

Download Primrose

Please make sure you have the Java Runtime Environment installed on your computer.

Citation

KE Ashelford et al. (2002) "PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database " Nucleic Acids Research, Vol. 30, No. 15 3481-3489

Please note that since publication of this paper, Primrose has been rewritten and upgraded to the Java version displayed on this page. The earlier Perl version (1.1.7) is still available from this site, however lacks some of the features of version 2.

Summary

Primrose uses data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides.

Please note...

Primrose was originally written for release 8.1 of the RDP database and works best with this database. The RDP database can be downloaded from here.

Licence

Primrose is open source software and is released under the terms of the GNU General Public Licence.

Program requirements

Primrose is written in Java, and will therefore run on any operating system capable of supporting this runtime environment. Java is available on Microsoft Windows, Apple Mac OS X, and other Unix platforms including Linux. Please refer to this page for further details. Note: Primrose requires Java version 1.4.x or later.

Help and tutorial

Click here for further information on Primrose, along with some examples.

Author and Contact details

This software was designed and written by Dr Kevin Ashelford. Any comments, suggestions or bug reports - please contact me at ashelford@cardiff.ac.uk.