Oligonucleotide alignment?

[drkoren]

I am trying to align my primers to the genomic sequence but the assembly parameters are not allowing all of my primers to align. Only approximately half align with modified assembly parameters (where I have changed the minimal overlap to 15). I have searched my genomic sequence in the contig file for the primer sequences and they are an exact match, so I know there are no errors. Can you recommend assembly parameters to make my oligonucleotides align to the genomic sequence?

Sincerely,
Koren

[Peter Richterich]

Koren,

You had the right idea with reducing the minimum overlap length. However, you will also need to reduce the minimum score from its default value of 20, for example to 10. With the default match score of 1, a minimum score of 20 means that you can only find oligos that are at least 20 bases long (and a perfect match).

If you need to match primers that are not perfect matches, you may also need to change the match scoring or penalties. However, that is not necessary for perfect matches.

Finally, make sure that the "Word length" is not too large - only matches that share at least one word of this length will be found. The default value of 12 should be fine, but if you have increased it, you may need to reduce it.

Best regards,

Peter

[drkoren]

Thank you, I will give that a try!

Koren