Search for exact matching of sequences

Search for exact matching of sequences using complement, reverse and reverse-complement

Usage

search_exact_seq_pq(physeq, seq2search)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

seq2search

A DNAStringSet object of sequences to search for.

Value

A list of data-frames for each input sequences with the name, the sequences and the number of occurrences of the original sequence, the complement sequence, the reverse sequence and the reverse-complement sequence.

Author

Adrien Taudière

Examples

data("data_fungi")
search_primers <- search_exact_seq_pq(data_fungi,
  seq2search = Biostrings::DNAStringSet(c("TTGAACGCACATTGCGCC", "ATCCCTACCTGATCCGAG"))
)