Degenerate Primer Sequence Recovery

Question

[james.nolan.2]

Hi all,

I am relatively new to much of the world of bioinformatics and am struggling with finding my degenerate primer sequences. I have some fastq files retrieved using MinION sequencing, and am struggling to find the two primer sets due to how degenerate they are.

Here are the two primer sets (5' - 3'): F: ATTCHACDAAYCAYAARGAYATYGG R: ACTATAAAARAAAYTATDAYAAADGCRTG

F: YTCHACWAAYCAYAARGAYATYGG R: ARTCARTTWCCRAAHCCHCC

I'm hoping someone would be able to help me with a tool to find these primers, or a script which could provide the various combinations for each primer set. Ideally this would be in python as it is the language I am most familiar with.

Thanks in advance, James.

[swbarnes2]

Do you know what regular expressions are? If not, maybe you should Google that.