Question: Alignement of 2 fast files already aligned
0
gravatar for ptitfab94
4 weeks ago by
ptitfab940
ptitfab940 wrote:

Hi guys,

I'm currently working on something, which is quite hard to me. Indeed, I have 2 fasta files already aligned, and I want to aligne the 2 fasta files wich contain protein sequences already aligned on BioPython.

Thank's for your help.

sequence alignment • 222 views
ADD COMMENTlink modified 21 days ago by Biostar ♦♦ 20 • written 4 weeks ago by ptitfab940

Apart from Pierre Lindenbaum comment, does it have to be with biopython? Several MSA software will do this as well (eg. muscle, t-coffee, ...)

ADD REPLYlink written 4 weeks ago by lieven.sterck5.5k

Yes, it has to be down on BioPython

ADD REPLYlink written 4 weeks ago by ptitfab940

Do you want to dealign and realign all the sequences, or do a profile-profile alignment?

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by jrj.healey13k

To realign what what previously aligned

ADD REPLYlink written 4 weeks ago by ptitfab940

Please make this easier on us. It's still not clear (maybe it's just me) what you want? As a general rule, if your question fits into a sentence or two, there's not enough information in it. Please at least provide some sample input data we can use, and ideally, some exemplar desired output.

Do you want to:

  • Take all the sequences from both alignments, de-align them all to get back to 'normal' sequences, and then create one 'super alignment'?

or

  • Select sequences from each alignment which previously aligned well and compute subsequent alignment?
ADD REPLYlink written 4 weeks ago by jrj.healey13k

Yes sorry if i'm not clear, it is exactly like "Take all the sequences from both alignments, de-align them all to get back to 'normal' sequences, and then create one 'super alignment'?"

ADD REPLYlink written 4 weeks ago by ptitfab940

Ok, that's quite straight forward.

Can you explain your requirement for BioPython more? Do the alignments have to be done with pure python, or are you allowed to use, for example MafftCommandline from within BioPython?

ADD REPLYlink written 4 weeks ago by jrj.healey13k

I don't know, we didn't have any indications about this. But I have never hear anything about the "MafftCommandline". So if you have both solution, with and without this this command, I would like to see !

ADD REPLYlink written 4 weeks ago by ptitfab940

we didn't have any indications about this

is this a homework / course assignment?

ADD REPLYlink written 4 weeks ago by lieven.sterck5.5k

It is a kind of "summer project", which is very long, and I am blocked to this specific part of the work.

ADD REPLYlink written 4 weeks ago by ptitfab940
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