Question: Batch pairwise alignment and consensus
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gravatar for lewis272727
14 months ago by
lewis2727270 wrote:

Hey, I have a few hundred forward and reverse reads, and I'd like to align them pair-by-pair and find the consensus of the alignment. Does anyone know of a way to do this? Even if someone knows how to do a batch pairwise alignment without the consensus that would be helpful.

The sequences are in FASTA format, I have already reverse complemented the reverse reads, so I just need something to go through them all and align two sequences at a time (with the end goal being a phylogenetic tree).

Thanks.

alignment • 407 views
ADD COMMENTlink modified 14 months ago by Michael Dondrup46k • written 14 months ago by lewis2727270
1

The consensus of a pairwise alignment isn’t possible/meaningful... how can you choose between one base or the other? Or are you just after all the sites which are identical?

Can you please elaborate the purpose?

ADD REPLYlink written 14 months ago by Joe14k

Yeah, I guess you could call it the conserved regions? All the bases which are identical once the sequences are aligned.

ADD REPLYlink written 14 months ago by lewis2727270

Why do you think this would be a good approach?

ADD REPLYlink written 14 months ago by WouterDeCoster41k
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gravatar for Michael Dondrup
14 months ago by
Bergen, Norway
Michael Dondrup46k wrote:

You might want to do a multiple sequence alignment instead (MSA). Try Jalview as a starter, or MAFFT maybe should be able to handle 100+ nucleotide seqs.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Michael Dondrup46k

But that will align all the sequences against each other right? I just want to align the forward and reverse to each other, 2 sequences at a time.

ADD REPLYlink written 14 months ago by lewis2727270

If they are going to align like that then what you are looking to do is to merge them into a longer representation, correct? I recommend bbmerge from BBMap suite.

ADD REPLYlink written 14 months ago by genomax73k
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