Bioinformatics toolkit

Download page

On this page are listed links to the various computer programs described on this web site. If you have any problems with this page, or the programs themselves, please let me know by emailing me at ashelford@cardiff.ac.uk.

The programs

All programs listed below are written in Java. Please ensure you have the Java Runtime Environment (JRE) installed on your computer. Further information on Java, and on downloading the JRE can be found by clicking here.

Program Summary Downloads1 Further information Reference
Mallard Screening ssu rRNA clone libraries for chimeras and other anomalies. Zip archive Click here Abstract
Pintail A ssu rRNA chimera detection tool. Zip archive | ClustalW2 Click here Abstract
Primrose 2 A ssu rRNA probe and primer design tool. Zip archive | Database3 Click here Abstract
OligoCheck Checking the effectiveness of ssu rRNA probes and primer sets. Zip archive | Database3 Click here -
OrientationChecker A simple tool for checking and modifying ssu rRNA sequence orientation. Zip archive Click here Abstract
OligoReport A tool for assessing probes. Zip archive Click here -
OligoLocator A simple tool for finding the location of probes or primers within sequences. Zip archive Click here -
TmCheck A melting temperature calculator. Zip archive Click here -
ReverseComplement A simple tool for determining the reverse, complement, and complement of any sequence. Zip archive Click here -
DatabaseViewer A simple program for viewing GenBank databases. Zip archive Click here -

1. Each zip archive contains the following:

  • A Java jar file to run the program (Mac OS X and Microsoft Windows users: mouse-click this file to start program).
  • A src directory containing source code (including an Ant build file).
  • A bin directory containing binary files used by the program.
  • A docs directory containing help and source code documentation.

2. Pintail also requires that the sequence alignment program ClustalW be installed on your computer. Click here for further information.

3. Although Primrose and OligoCheck will work with any Fasta or GenBank formatted sequence database, it was originally designed to work with the RDP release 8.1 database. Although this database is now somewhat out-of-date, it is still useful, containing as it does phylogenetic information that Primrose can display as an expandible phylogenetic tree.

Known issues and bug fixes

If you come across a bug, please let me know and I will try and correct it as soon as possible - email me at ashelford@cardiff.ac.uk.

Archive

Primrose 1.1.7 (includes Rose). Size 9.6 Mb. Note this older version of the program has been superseded by Primrose 2, above.

This earlier version of Primrose appeared in the following research paper:

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

Primrose, version 1, was written in Perl, using the Perl port of the Tk GUI library. The archive file includes the Perl 'source code' and executable versions of Primrose and Rose for Microsoft Windows only.