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  • Protein annotation parameters (query or subject coverage?)

    Hi there.

    I am annotating some proteins' functions and I a have some doubts about the parameters I should use. I'm using e-value below 1x10-4, identity above 40% and coverage above 70%, but I don't know if a sould use the query coverage or the subject coverage for annotation.
    I only saw the query coverage being used (the % of your query sequence that overlaps the subject sequence), but it makes more sense to me and some colleagues to use the subject coverage (the % of the subject sequence that overlaps your query sequence). Since the protein with the known function is the subject one, if you find most of it within the query coverage it means that your query protein has higher probability to share the subject protein's function.
    If some one could explain why I sould use the query or the subject coverage I would be very greateful (sorry if it is an obvious question).

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