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Citation

KE Ashelford et al. (2005) "At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies." Applied and Environmental Microbiology, (12): 7724-7736.

Summary

Pintail is a tool for identifying anomalies, including chimeras, within 16S rDNA sequences. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene.

Licence

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

A quick guide to using Pintail

1. Enter the 16S rRNA gene sequence to be investigated into the text box marked 'query sequence'.
2. Enter a reliable 16S rRNA gene sequence in the text box labelled 'subject sequence'.
3. Click 'Run' to carry out the analysis.

A chimera is indicated if the plotted observed percentage differences line deviates significantly from the expected percentage difference line. This deviation is quantified with the Deviation from Expectation (DE) statistic. The program determines whether the calculated DE value is likely to be indicative of a chimera (or other sequence anomaly) and provides an assessment accordingly.

For a more detailed explanation, click here for a tutorial on Pintail.

Program requirements

Pintail 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: Pintail requires Java version 1.4.x or later.

In addition Pintail uses the sequence alignment program 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/. Click here for further details.

When running Pintail for the first time you will be presented with the following dialog box:

Dialog box (as viewed on Mac OS X).

Simply click the 'Find ClustalW' button and identify the location of the clustalW executable with the resulting dialog box.

Summary of required downloads

• Click here to download Pintail.
• Click here to download the Java Runtime Environment.
• Click here to download ClustalW.

Help and tutorial

Click here for a tutorial on Pintail. In this tutorial, the known SSU rRNA chimera AY297986 is investigated.

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.

This work has been supported by the Biotechnology and Biological Sciences Research Council (BBSRC).