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Summary

The ability of nucleic acid primer sets and probes to bind exclusively to the correct nucleic acid sequence is fundamental to the accurate targeting of specific phylogenetic groups. Such specificity depends largely on the uniqueness of the region of nucleic acid sequence these oligonucleotides target. The more unique the region, the more robust will the primer set or probe be in annealing only to the intended target, even if variations in annealing temperature and other biochemically relevant parameters result in the oligonucleotides binding successfully with targets with one or more base differences. Thus, a robust primer set or probe can be viewed as one that anneals exclusively to its intended target even when one or more mismatches are allowed.

OligoCheck is designed to assess this robustness, by assessing a primer set or probe's phylogenetic range as the number of base-mismatches with potential target sequence increases. The user supplies a primer set or probe to check, along with a database of nucleic acid sequences. OligoCheck checks the primer set or probe against each relevant record in the database and notes whether matches occur with an increasing number of base mismatches allowed.  The resulting analysis is displayed in a graphical form alongside the sequence-record data.

Licence

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

Program requirements

This program 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: this program requires Java version 1.4.x or later.

Help and tutorial

Click here for further information on OligoCheck, 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.