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All posts created by rspence
| Link to this post | posted 07 Oct, 2020 01:52 | |
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Thank you Debbie "Percent Coverage" in NCBI refers to Percent Identity and not Query Coverage "Percent Alignment" in HHPRED refers to (Target Length /Query Length) |
Posted in: Notes and Final Files → Coverage and Alignment
| Link to this post | posted 06 Oct, 2020 19:55 | |
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Annotation for "Blast-Start" asks for coverage. This implies the % number under "Query Coverage" on the NCBI website and not the % alignment? Annotation for "SIF-HHPred" ask for % alignment. How exactly do I calculate this? HHPred gives me "Aligned Cols" and "Target Length". I also have the number of AA from my input sequence. |
Posted in: Notes and Final Files → Coverage and Alignment
| Link to this post | posted 20 Sep, 2020 19:18 | |
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okay, thanks for the quick reply! |
Posted in: Frameshifts and Introns → Frameshift K6
| Link to this post | posted 20 Sep, 2020 19:03 | |
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Identified the frameshift but I am unsure if its -1 or +2. Yellow highlight, frame 1, AAs: IEGK then it should jump to frame 3 (soon to be blue highlight) and continue AA: ISQV It seems to me that the slipper sequence "GGGAAAA" final "A" 11670 is counted 2x. The final "A" in codon for amino acid "K" and again as the first "A" in codon for amino acid "I" I though this is the definition of a -1. However, when I learned how to read the 6 different frames I thought moving down 2 frames is a +2? |
208KbPosted in: Frameshifts and Introns → Frameshift K6