Hi, my name is Henry Luo. I am NCU master student from Taiwan. I need some help. Recently I do my project about probe design to detect environmental bacteria, and I have used DECIPHER package on my R session. I have used some functions on my project to do probe design, including "OrientNucleotides", "AlignSeqs", and "DesignArray". I use these functions on 16S rRNA of my target species named Dehalococcoides mccartyi 195 and I finally got some great results. Now I have 75 sequences and they are 19-mer and 20-mer. I want to do filtration and verification on these 75 sequences. Is affy package applicable in my project about environmental bacteria? Are there some other DECIPHER functions which can be used to filter and verify these 75 subsequences? Are there other Bioconductor packages applicable in my next step of my project? My next step is trying to use these 75 subsequences to do probe design. I want to select unique probes and group probes from these 75 subsequences. Finally I will use these probes to do specificity validation, and I want to get the best probe sets as candidate probes, and I can build probe database to do microarray construction and evaluation. I hope there are some affy functions and DECIPHER functions which can be used in my next step of my project. I hope there are other Bioconductor packages which can be used in my next step of my project. Thank you.

Best regards,

Henry Luo