Bioinformatics Toolkit - software tools for analysing 16S rDNA gene sequences, including tools for chimera detection and primer and probe design.

The bioinformatics toolkit is a collection of free, open source, software tools, written in the Java programming language, for analysing 16S rRNA gene sequence data. Includes tools for chimera detection and probe & primer design. Programs in this toolkit will run on Microsoft Windows, Apple Mac OS X and Unix/Linux operating systems.

What does it contain?

Mallard - a tool for identifying 16S rDNA chimeras, and other sequencing anomalies, within multiple sequence alignments. Download now.
OrientationChecker - a simple, fast, tool for determining the location and orientation of 16S rDNA partial sequences. Download now.
Pintail - a tool for identifying 16S rDNA chimeras and other sequencing anomalies. Download now (requires ClustalW).
Primrose - a 16S rDNA probe and PCR primer design tool. Download now.
OligoCheck - a tool for checking the phylogenetic range of 16S rDNA PCR primer sets and probes. Download now.
TmCheck - a melting temperature calculator for 16S rDNA probes and primers. Download now.
OligoLocator - a simple tool for locating probe and primers within sequences. Download now.
OligoReport - a tool for assessing 16S rDNA probes. Download now.
DatabaseViewer - a simple tool for viewing database records. Download now.
ReverseComplement - a simple tool for determining the reverse complement of sequences. Download now.

How can you get it?

The toolkit, including database files, help and tutorials can be downloaded by clicking here.

What else might you need?

Programs in the toolkit are written in the Java computer language, and will therefore run on any operating system capable of supporting the Java Runtime Environment (JRE). Java is available on Microsoft Windows, Apple OS X, Linux and other Unix platforms. Please refer the Java website or click here for further details.

In addition, Pintail uses Clustalw, so this will also need to be installed on your computer. Clustalw executables for Microsoft Windows, Mac OS X and Unix platforms are available from the EBI FTP Server at ftp://ftp.ebi.ac.uk/pub/software/. Alternatively, click here for further details.

Contact details

All the software presented here was designed and written by Kevin Ashelford. Any comments, suggestions or bug reports, please contact me at ashelford@cardiff.ac.uk.