Sequencing Of Pcr Products

Question

[Pierre Lindenbaum]

I've received the sequences of a pool of PCR products (in grey)

I've got the sequences of the primers. Those sequences can overflow the sequence of the final pcr product.

A primer 'A' is not always in front of the same primer 'B' (eg. green primer ).

What tool(s) would you use to find the best pair of primers that would align with the PCR product and extract the sequence between the two primers ? (in yellow)

Thanks,

Pierre

[Devon Ryan]

How many adapters are we talking about? I know that cutadapt can be fed an arbitrary number of adapters and it will just trim off the best match. However, you have to specify them on the command line, which could become unwieldy.

Answer 1

[Pierre Lindenbaum]

OK, here is how I've processed my problem today:

make a blastdb for the forward sequences.

make a blastdb for the reverse sequences.

for each sequence get the best Hit forward and the best Hit reverse, get the location of the best Hsp and extract the region between the two hsp.

It works fine so far.

Answer 2

[Istvan Albert]

As dpryan79 mentions, adaptor trimming tools like cutadapt

I had a link in my bookmarks to a page that lists a number of such tools http://bioscholar.com/genomics/tools-remove-adapter-sequences-next-generation-sequencing-data/

[Pierre Lindenbaum]

cutadapt doesn't fulfill my needs: the sequence of the primer are very long and it's not easy to find the 'best' primer that matches the sequence