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  • How to trim multiple alignment?

    I have a specific problem. We want to discover isoforms of a gene based on long reads. We have a population of overlapping sequences all under 1000bp. I aligned them with Clustal, and now would like to trim the edges so that only common area for all sequences is remained.
    So, I need to convert alignment like this:

    >>>>>>>>>>atgcatgcatgcqtgatgctgatgctagtgctagtgctagtcgtagctga
    gcatgcatgcatgcatgcatgcqtgatgctgatgctagtgctagtgcta
    >>>>>>catgcatgcatgcatgcqtgatgctgatgctagtg
    >>>>>>>>>>>>gcatgcatgcatgcqtgatgctgatgctagtgctagt



    to
    atgcatgcatgcqtgatgctgatgctagtg
    atgcatgcatgcqtgatgctgatgctagtg
    atgcatgcatgcqtgatgctgatgctagtg
    atgcatgcatgcqtgatgctgatgctagtg


    Is there a way to do that in Linux? Right now the alignment is in CLC Bio, but I can export it to SAM/BAM or possibly to text as well.

    My understanding is that if I trim produce a text file with the alignment, I can then run uniq -c command in Linux and get both unique sequences in my list, and counts (-c) for each of them.

    Any advise on how to do that best are appreciated. I am not too handy with PERL or Python though, so shell scripts or some unix tricks would be more desirable.

    Thanks!

    Thanks for any input

  • #2
    Avoiding Perl or Python (which is how I would do this), many biologists I know used to or still use BioEdit for that kind of thing, but it is Windows only and dead software. You might try JalView http://www.jalview.org/ or UGENE http://ugene.unipro.ru/ which are both free, open source and cross platform.

    Comment


    • #3
      Thank you for the reply. I can certainly do simple Perl and Python, but I am not sure how to approach the problem. If you have ready to use scripts, I'd appreciate your posting them here.
      Thanks!

      Comment

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