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  • What to do after LALIGN? Best hybridization?

    Hello,

    I've been experimenting with various open source bioinformatics programs that are available, and have just finished compiling results from LALIGN (waterman scores) for aligning an miRNA sequence with various protein mRNA sequences. I have also gone ahead and seen where my RNA sequences are aligned using mFold.

    I am assuming that scores of 85-90% identity in LALIGN are strong, and the next step would be to identify the ideal locations of hybridization.

    Since I have multiple molecules with local alignments for the same miRNA, I was hoping to receive some help as to how I can determine which local alignments would be better than others, and by how much.

    I appreciate any input.

    Thanks.

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