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% alignment

| posted 11 Feb, 2021 20:00
For the BLASTp analysis done in assessing the start site, should we be reporting % SUBJECT or QUERY aligned?  DNA Master reports % SUBJECT aligned but NCBI lists % QUERY coverage.  For most cases, this will not matter as they will be at or near 100% aligned for both query and subject.  Or maybe it does not matter for this purpose, when it is used to help evaluate start site choice?

I don't recall being asked this in the past or having a discussion about it. We have always used the % SUBJECT aligned value from DNA Master except when we went to NCBI or phagesdb.

I cannot find a clear statement about which should be recorded.
| posted 15 Feb, 2021 17:07
It doesn't matter, just state (maybe in your cover letter) what you used.
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