Alignment of 2 fasta files already aligned
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 align the 2 fasta files which contain protein sequences already aligned on BioPython.
Thank's for your help.
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Apart from Pierre Lindenbaum comment, does it have to be with biopython? Several MSA software will do this as well (eg. muscle, t-coffee, ...)
Yes, it has to be down on BioPython
Do you want to dealign and realign all the sequences, or do a profile-profile alignment?
To realign what what previously aligned
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:
or
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'?"
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
MafftCommandlinefrom within BioPython?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 !
is this a homework / course assignment?
It is a kind of "summer project", which is very long, and I am blocked to this specific part of the work.