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Coverage and Alignment

| posted 06 Oct, 2020 19:55
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 06 Oct, 2020 20:17
When documenting Blast-Start, you will want to address that you are choosing a start that aligns to others' calls. The % coverage is asking you to note that you have % identities? Did you match the whole length of the protein or just a part of it. It should also include that you matched the start 1:1 (or whatever the alignment is).

The note in the Bioinformatic Guide about % alignment in the HHPred results is :
"%alignment" here refers to the % of the query protein that is aligned to the target sequence. you will need to calculate this by hand, as HHPred does not report it as a number for you, it merely reports the length of your sequence that is included in the alignment. Divide this number by the full length of your query sequence.

Estimates of that % would be great!
| posted 07 Oct, 2020 01:52
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)
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