[Biopython] clustalw align multiple sequences to reference.

[A M Torres, Hugo]

I am having the same problem. First I was running "needle" on each
sequencing data and its reference then I thought of generating a big fasta
containing all sequences and then running MUSCLE. Like Daniel Jones I don't
mind that sequences are aligned against each other but they should be
aligned properly against the reference sequence.

On a side note: I have sequenced DNA data which I need to align to a
reference sequence and look for mutations. I am confused. Should I use a
global alignment algorithm or a local alignment algorithm? I have data for
forward and reverse strands, so it could be useful if I had both aligned
with the reference in a single file.

I don't mean to hijack the thread, but this seems exactly like my problem.
Excuse me for any inconvenience.

Hugo Torres

On Wed, Jul 13, 2011 at 6:44 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wednesday, July 13, 2011, Daniel Jones <lawson.jones at gmail.com> wrote:
> > Hi Biopython users,
> > I have a file with many (~50,000) 200 bp sequences, each of which I would
> > like to align to a fixed reference sequence. I *don't* care about
> aligning
> > all 50,000 sequences with each other; I only care about aligning each one
> > with the reference sequence. I can't figure out a way to do this without
> > generating 50,000 files, which seems like ridiculous unnecessary
> overhead.
> > It seems like ClustalW's interface is quite inflexible in demanding
> separate
> > input and output files for each alignment, but I don't have much
> experience
> > using it so maybe I'm completely missing something.
> >
> > Incidentally, I'm not wedded to the idea of using ClustalW, so if there's
> an
> > alternate alignment program that would make this easier, I'd certainly be
> > open to trying it.
> >
> > Thanks,
> > Daniel Jones
>
> You need a pairwise alignment tool. Perhaps needle or water from the
> EMBOSS suite, or Biopython's pairwise2 module would be suitable (not
> in the tutorial, read the API docs).
>
> However, as Eric suggested, an NGS alignment tool might be more
> appropriate.
>
> Peter
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