Find patterns in DNA sequence

Question

[kindlychung]

I want te be able to count the number of occurrences in a given sequence (for example ACTTTAG) in the GRCh38 reference genome. Is there an existing tool for doing this? Thanks!

Answer 1

[dago]

You can use Biostring in Bioconductor.

The function countPattern should do the job. Just check if it is using a sliding window or not.

Answer 2

[5heikki]

Jellyfish is pretty nice for kmer counting.

Answer 3

[dariober]

I wrote a simple script for finding patterns (regular expressions in fact) in fasta files, it's fastaRegexFinder.py and I also happen to mention it in this post Quadruplex sequence batch prediction

If you just want to count the number of occurrences you can do

fastaRegexFinder.py -f genome.fa -r 'ACTTTAG' | wc -l

Answer 4

[Antonio R. Franco]

You can also use bowtie1.

It is specially nice in finding (mapping) short sequences..