Pintail

Pintail is a free and open-source Java-based application that enables you to identify and examine 16S rRNA chimeras, along with other types of anomalies. It compares evolutionary distances between a query and subject sequence.

Setting up the environment

The downloaded package is not wrapped in a setup kit, so you can extract the archive files and simply double-click the JAR executable file to launch the tool. Apart from Java, you must have ClustalW, a program used for sequence alignment.
It's necessary to indicate the full path to ClustalW. Pintail automatically identifies its executable file by name, which means that you must rename it to "clustalw.exe" if it's different.

Set query and subject sequences to render plots

Concerning the interface, the utility adopts a single window with a straightforward look that contains text boxes for entering query and subject sequences (5'-3'; sense). Both fields must be filled with information in order to generate the plot.
It's possible to change the default window and step size, as well as to view, print and export the graph (to PostScript, JPEG or PNG format) representing the base position in the 16S rRNA gene.

Examine, print and export data

Displayed information explains the graph with observed and expected differences, including deviations from expected differences (DE) observed between previously analyzed type-strains (% of type-strain comparisons and maximum DE), demonstrations, and conclusion (e.g. strong evidence of a sequence anomaly).
There are buttons for undoing and redoing actions, as well as for cutting, copying, pasting, pasting, and selecting all data. Plus, you can choose between three UI themes and hide tooltips from the GUI. Help documentation is available, which includes a tutorial and the official IUB base codes for your reference.

Conclusion

Pintail is packed in a user-friendly interface and features approachable options for detecting possible sequence anomalies 16S rRNA chimeras and others. It worked smoothly in our tests and rendered plots swiftly. However, it requires a bit of investigation and tinkering to set up the environment.