Counting repetitions of a sub-sequence.

[mgrant...@gmail.com]

Hi,

Sorry for the newbie question.

I am trying to do something simple, and unfortunately I am not familiar enough with go to figure an easy way to do it.

I am reading a fasta file, and I need to determine how many times a certain sequence is repeating.

Can someone possibly suggest a way?

Thanks for your time.

   Michael

[Dan Kortschak]

By "repeating" and "sequence" what do you mean?

How long are the expected repeats and how perfect is the requirement for matching between repeats?

[mgrant...@gmail.com]

I am looking for something similar to biopython's Bio.motifs. In my analysis case the subsequences are short (about 5-10 letters), and I am looking for perfect matches only.

Before using this library I used strings.Count.

[Dan Kortschak]

I think your best bet would be the index/suffixarray package in the standard library then. (There is a PWM package in biogo that handles cases a small as yours, but it does more than what you want here). You will need to convert the sequence letters to []byte, but alphabet.Letters can be converted with essentially zero cost using alphabet.LettersToBytes.

I have partially implemented a BWT search, but it is nowhere near ready.

Dan

[Michael Grantham]

Thanks!