<p>Hello,</p>

<p>I want to compile a BED file with all genomic regions where I find a given sequence (say, I have a 10-nucleotide sequence, and 10^9 nucleotides in the genome). I have previously tried solving this task with a weight matrix based approach, but it takes too long. So I decided to simplify the task: just a fixed sequence, no mismatches. I am thinking of something like Bowtie, but with all non-unique hits reported. Looks like a pretty simple task. Did someone tried solving this?</p>

<p>Thanks!</p>

<p>It&#39;d probably be faster to just use Biopython. Iterate over the entries in a fasta file, and use find iteratively to produce all of the found regions.</p>
