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  • xuhanhan
    Junior Member
    • Jul 2010
    • 3
    #1

    EST EST alignment

    Dear all,

    I work on a plant without genome sequences, and got a large amount of 454 RNA-seqs.

    Right now I am trying to identify the indels abover 50 nt among these ESTs. I am appreciated if anyone could give me the suggestion on program to solve my problem.

    I already tried Blat and Megablast, but they would break into more than one alignments if there are indel above 50 nt.

    Thanks

    Hanhan
    Tags: est est alignment, large indels
  • xuhanhan
    Junior Member
    • Jul 2010
    • 3
    #2
    EMBOSS tool EST2Genome can align large indels. But it just could be used to find large indels in hit sequences.

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