DECIPHER Probe Design Questions
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@henry1995910343-24214
Last seen 4 days ago

Hi, I recently use DECIPHER on nine 16S rRNA and eight functional genes to do microarray probe design. First I combine these target genes as DNAStringSet, and I use DECIPHER function named "OrientNucleotides" on my DNAStringSet to check the orientation of my target genes. Second, I use DECIPHER function named "AlignSeqs" on my DNAStringSet to align my target genes because I think their sequences lengths are different. After this, these target genes of my DNAStringSet are the same, and I use DECIPHER function named "BrowseSeqs" on my DNAStringSet and it showed a "webpage" which included these target genes and a "consensus". What is its meaning? Finally I use DECIPHER function named DesignArray on my DNAStringSet which has been aligned, and I get 151 microarray probes, but these probes connecting poly-T tail. What's the meaning of poly-T tail connecting these probes? Questions:

  1. Is DECIPHER function AlignSeqs applicable on target genes of my DNAStringSet? What's the purpose and meaning of function AlignSeqs?
  2. What's the meaning of DECIPHER function BrowseSeqs when it showed a webpage about my target genes and "consensus"?
  3. When I use DECIPHER function named DesignArray on my DNAStringSet, should I use function AlignSeqs on my DNAStringSet first? The results of DesignArray on my DNAStringSet with or without AlignSeqs, which one is better?
  4. Why are these poly-T tail connecting on every microarray probes? Does poly-T tail affect the specificity and sensitivity of my microarray probes?

Thank you.

Best regards,

Henry Luo

DECIPHER • 15 views
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