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  • Selection of sequences

    While having multiple sequences with same sequence except one or two additional base pairs at the start or end, how to remove the duplicates (not exactly duplicates). Hope you understand my point.

    Please find the following example sequences. I just need to select one sequence from the 5 sequences, the longest one COC9.

    COC5 AAAAAGCAGGGTCACCTTGTGTCCTTAAA
    COC6 AAAAAGCAGGGTCACCTTGTGTCCTTAAAC
    COC7 AAAAAGCAGGGTCACCTTGTGTCCTTAAACC
    COC8 AAAAAGCAGGGTCACCTTGTGTCCTTAAACCT
    COC9 AAAAAGCAGGGTCACCTTGTGTCCTTAAACCTA

  • #2
    Code:
    usearch -derep_prefix input.fasta -output derepped.fasta
    USEARCH
    savetherhino.org

    Comment


    • #3
      Originally posted by rhinoceros View Post
      Code:
      usearch -derep_prefix input.fasta -output derepped.fasta
      USEARCH

      Thanks rhinoceros.,

      But i am new user to this type of commands. I am using windows platform. I have downloaded the program usearch from the website as you just mentioned. But while running the programme, the programme is closing immediately. Please help me regarding this,

      Thanks in advance.

      Comment


      • #4
        I can't really help you there. I haven't used Windows for many years. Did you read the manual? If you never used command line before also see this section.

        Good luck
        savetherhino.org

        Comment


        • #5
          Thanks

          Thanks Rhinoceros.
          It got worked. I have done as the guidelines provided. Thank you verymuch. I was searching like this for the past ten days. Finally i got here from you. Thank you verymuch once again.

          Comment

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