For point mutation idenfication

[rongming liu]

Hi Torbjørn,

I have generated a error prone PCR based library for a protein. Then, I have done pacbio sequencing which each reads can have ~4000 bp which is simiar to the template. Could I use vsearch to do the aligment? Then could I get the surmary which point mutation is top hits? 

Best,

Rongming

[Colin Brislawn]

Hello Rongming,

For this alignment, is your protein represented as a .fna nucleotide sequence or a .faa amino acid sequence? Vsearch only works with nucleotide sequences, so you would have to reverse translate your .faa amino acid sequence before you could perform this alignment using vsearch.

If that workflow works for you, let's see what Torbjørn recommends for finding point mutations!

Colin

[Torbjørn Rognes]

Hi

I need some more information on what you are actually doing to be able to help you.

As Colin pointed out, vsearch only works on nucleotide sequences, not proteins.

You can make DNA alignments with vsearch, but I do not know if it is the ideal tool in this context.

- Torbjørn