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. 2008 Jan;2(1):23-31.
doi: 10.1111/j.1750-2659.2007.00031.x.

The Influenza Primer Design Resource: a new tool for translating influenza sequence data into effective diagnostics

Michael E Bose  1 , John C Littrell, Andrew D Patzer, Andrea J Kraft, Jacob A Metallo, Jiang Fan, Kelly J Henrickson
Affiliations

The Influenza Primer Design Resource: a new tool for translating influenza sequence data into effective diagnostics

Michael E Bose et al. Influenza Other Respir Viruses. 2008 Jan.

Abstract

Background: Recent outbreaks of highly pathogenic avian influenza and multiple occurrences of zoonotic infection and deaths in humans have sparked a dramatic increase in influenza research. In order to rapidly identify and help prevent future influenza outbreaks, numerous laboratories around the world are working to develop new nucleotide-based diagnostics for identifying and subtyping influenza viruses. While there are several databases that have been developed for manipulating the vast amount of influenza genetic data that have been produced, significant progress can still be made in developing tools for translating the genetic data into effective diagnostics.

Description: The Influenza Primer Design Resource (IPDR) is the combination of a comprehensive database of influenza nucleotide sequences and a web interface that provides several important tools that aid in the development of oligonucleotides that may be used to develop better diagnostics. IPDR's database can be searched using a variety of criteria, allowing the user to align the subset of influenza sequences that they are interested in. In addition, IPDR reports a consensus sequence for the alignment along with sequence polymorphism information, a summary of most published primers and probes that match the consensus sequence, and a Primer3 analysis of potential primers and probes that could be used for amplifying the sequence subset.

Conclusions: The IPDR is a unique combination of bioinformatics tools that will greatly aid researchers in translating influenza genetic data into diagnostics, which can effectively identify and subtype influenza strains. The website is freely available at http://www.ipdr.mcw.edu.

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Figures

Figure 1
Figure 1
Diagram of the process for using the Influenza Primer Design Resource website. First, the user searches the database for the sequences they are interested in. They then select the sequences that they are interested in. Finally, they set up the parameters for determining the consensus sequence and the Primer3 analysis. The results are returned to the user via email.
Figure 2
Figure 2
An example of the results returned by Influenza Primer Design Resource. The sequence conservation results display the consensus sequence, conserved regions, percent conservation and sequence polymorphism information.
Figure 3
Figure 3
The primer/probe database blast results show the published oligos that matched the consensus sequence in a graphical view aligned with the sequence (A) along with a table of published information about the oligos and information from the blast results (B).
Figure 4
Figure 4
The Primer3 results display the oligos selected by Primer3 for the consensus sequence based on the user‐entered parameters. The resulting oligos are displayed aligned with the consensus sequence with a summary of the oligo information in a table below.
See this image and copyright information in PMC

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