Then choose one region as the template (Chosen template:Region 7: Position 850 to 1300,Segment Length: 451).Ģ.3 Then use the chosen one region as template for real-time PCR primer and probe design. The result will show how many conserved regions found and details of each region. This process is needed because mutation rate in HA gene is high.įile> New Alignment> File> Import> Sequence alignment file> choose text file that save the FASTA sequences.Ģ.2 Find conserved regions in the HA sequencesĬhoose all sequence> Accessory Application> ClastalW Multiple alignment> Run ClastalW> OK> Alignment> Find Conserved Regions> Start Use BioEdit program to find conserved regions in the HA gene for template using. Retriving the HA nucleotide sequence of swine influenza from the. HA gene is chosen because HA and NA gene do not conserve between influenza subtype.ġ. Swine-Origin Influenza A (H1N1)from other influenza subtypes. HA gene of influenza virus is chosen for primers design which can be used to distinguish between 2009 Please also describe what are gene(s)/region(s) that you choose? And give us the reason why? The real-time PCR primer and probe set(s) which can be used to distinguish between 2009 Swine-Origin Influenza A (H1N1)from other influenza subtypes. Please use the bioinformatics tools to design these following items ġ.
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