How to count the kmer occurrence in FASTA file considering overlapping and reverse complement? I am using count_overlap() for counting the kmers from Biopython .
Does it take the reverse complement of kmer into account?
I need to count reverse complement too
There's a lot detail missing here, but at a guess could you try,
from Bio import SeqIO
from Bio.Seq import Seq
for record in SeqIO.parse(&quot;ls_orchid.gbk&quot;, &quot;genbank&quot;):
    reversec = record.seq.reverse_complement())
    revcount = reversec.count_overlap('AT')
    print (revcount + count_overlap('AT'))

Essentially count_overlap only counts the forward strand if this is the Biopython method. Not debugged the above.