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  • How to connect shared sequences in two large fasta files

    Hi,

    I would like to hear any suggestion on connecting two fasta files, here is my problem:

    I have two large fasta files, each around 1GB.

    F1.fasta contains:
    AB001.1
    GTAGTGTGAGGTGTGT
    AB002.1
    GTAGTGTGAGGTGTGT
    AB005.1
    GTAGTGTGAGGTGTGT

    And F2.fasta contains:
    AB005.2
    GTAGTGTGAGGTGTGT
    AB006.2
    GTAGTGTGAGGTGTGT

    Imade up the sequences. But as you can see, they are actually pair-end reads from illumina HiSeq. The files were trimed so contain difference number of sequence. Now I wonder if there is any program I can used to find the paired sequnece (i.e. AB005.1 + AB005.2), and put a string of "--------------" between them.

    So the output fasta will look like
    AB005
    GTAGTGTGAGGTGTGT-------------------GTAGTGTGAGGTGTGT

    I would appreciate if you can guide me to any program or any command i can use in R or python?

    Thanks!

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