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How Do I Get The Frame For A Translated Search? |
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Answer» I'm using Bio::Search* and its frame() to parse BLAST but I'm seeing 0, 1, or 2 instead of the EXPECTED -3, -2, -1, +1, +2, +3. Why am I seeing these different numbers and how do I get the frame according to BLAST? These are GFF frames - so +1 is 0 in GFF, -3 will be ENCODED with a frame of 2 with the strand being set to -1. $hsp->hit->strand; I'm using Bio::Search* and its frame() to parse BLAST but I'm seeing 0, 1, or 2 instead of the expected -3, -2, -1, +1, +2, +3. Why am I seeing these different numbers and how do I get the frame according to BLAST? These are GFF frames - so +1 is 0 in GFF, -3 will be encoded with a frame of 2 with the strand being set to -1. $hsp->hit->strand; |
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