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  • arkal
    advancing one byte at a time!
    • Jun 2011
    • 56

    #1

    GlimmerHMM output

    Hey guys,

    I'm using glimmerHMM to predict genes from a genome. I'm curious about the concept of the negative strand. Take the example file below

    GlimmerHMM
    Sequence name: ABCDE
    Sequence length: 580 bp

    Predicted genes/exons

    Gene Exon Strand Exon Exon Range Exon
    # # Type Length

    1 1 - Terminal 139 144 6

    Since it lies on the negative strand, does it mean that the region begins at position 139 (on a 1 to 580 scale) moving forward or from position 580-139+1 = 442 going backwards?

    Sorry if this is something trivial i've overlooked,

    Thanks in advance,
    -A

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