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  • MUltifasta file

    hi every one,

    what i need to do is i need multiple sequence alignment file

    i converted the vcf file to consensus fasta and "cat" all these consensus sequence into multifasta.



    in my cat file seq are >1......>10000 for a.fasta and >1......>10000 for b.fasta when i use clustal w it gives error that sequence have same header THAT MAKES SENSE so what i am planning to do is to convert >1..>2...>3.>10000 to >1

    and >1..>2..>3..>10000 for b.fasta to >2 and same for for all my 5 samples
    i have to use this file for multiple alignment
    Regards
    Last edited by huma Asif; 09-08-2014, 10:13 AM.

  • #2
    Do you want to know how to do the renaming or is this just an informational post?

    Comment


    • #3
      how i can convert
      >1...>2....>3...>10000 to >1

      and
      >1..>2..>3....>10000 for b.fasta to >2 and
      same for for all my 5 samples
      i have to use this file for multiple alignment
      Last edited by huma Asif; 09-08-2014, 10:28 AM.

      Comment


      • #4
        You want to convert every fasta ID header from multiple fasta sequences in file "a" to >1 and from file "b" to >2, is that correct?

        Comment


        • #5
          Originally posted by GenoMax View Post
          You want to convert every fasta ID header from multiple fasta sequences in file "a" to >1 and from file "b" to >2, is that correct?
          That won't give them unique deflines, which I think is what he/she is after for input to clustalw. I still can't tell what the problem is, though.

          Comment


          • #6
            GenoMax
            yes

            Comment


            • #7
              If you rename all of them as >1 or >2 for a sample the sequences ID's would no longer be unique.

              What kind of MSA are you trying to do?

              Comment


              • #8
                i want all the genes e.g in sample 1 to be concatenated as >1 likewise for my all samples
                my thought is as all genes in all files are in same order so when i have multifasta as >1, >2, >3,>4,>5
                i will take that multifasta to do alignment around these interval

                Comment

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