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Overview

ThDyHibr is a program for simple modeling of primers/probes hybridization on to a set of target sequences. It aim for relatively rapid and simple selection of candidate primer and probes for PCR and microarray detection and identification of RNA viruses. Although it don’t need the target sequences to be aligned, it can take advantage of low quality alignments (like the ones obtained by simple BLAST queries at the NCBI site) to set common coordinates for selection (and report) of the genomic region to analyze. The expected user is directly the biologist that need the new assay. The program need to be easy to use (with a graphical user interface - GUI) and install. Actually, no installation is need – just run the supplied executable. No modification of the computer system will occur and thus no admin right are needed.

Motivation

I have been working on RNA virus detection by PCR since 1993, and have observed the following pattern in the workflow for new assay design:

A research (which basically is a molecular biologist working with a "new" virus) decides he need a new diagnostic or screening PCR. He will collect available sequences from the NCBI GenBank site and from personal sources and build a multialignment. Taking into account this alignment and information from experiments and the published work from other authors a promising region within the genome will be chosen. Some free or commercial software will help to choose a set of primers or probes to test experimentally and to select the ones that will be further used. Among many other, some of the difficulties frequently found are:

• Too many sequences to align.
• Too few sequences to align.
• High variability (the sequences are more than 15-30 % divergent - in % of point differences)
• The software only process one sequence at once.
• The parameters are difficult to select because they are text-based, expert-experience based, etc. (number of mismatch to allow, maximum Tm difference between primers, etc.)

Due to these difficulties, a common practice has been to print the alignment and visually decide a set of candidate primers and probes, which are then partially cheeked with the software and submitted to the experiemnts.

Many of these problems have been addressed by the writings and software of Santa Lucia et al. Lebers and Kaderali et al. adapted the dynamic the dynamic programic algorithm if

GUI manual