I am trying to findPalindromes in a whole gene sequence and to save them to then look for overlaps of these with mismatched nucleotides between two organisms for designing specific strain qPCR probes and primers. I've tried saving them as a data frame from findPalindrome() and exporting via export.fasta() from bios2mds package but the data frame only has one column with the palindromes and not the locations. Can you help me?
I am new to programming and bioinformatics so sorry if its a dumb question or an obvious answer ;-)
All the best! Vicki