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I'm doing some research about a proteïne which is sequenced, however Í'm not able to find any information about the score which ProSite scan shows after finding an possible domain profile.
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I have read the prosite help, however there isn't anything which explains what the score means.

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The score provides an indication of well a specific profile (which is a weight matrix) matches the profile for the domain. Section II.B. Profiles development explains this in further detail.

A paper that outlines the development of PROSITE notes that they primarily use a cut-off of 8.5 and explains the score thus;

the raw scores in PROSITE profiles are converted into so-called ‘log10 per residue E-values’, allowing the computation of the number of expected matches with equal or higher score in a database of a given size. For instance a match with a normalised score of 9.0 or higher is expected to occur about once in a database of one billion residues.

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  • $\begingroup$ Why isn't it just an E-value just like in BLAST? I read your references but I can't get it clear. Do you know how it's calculated? @Michael_A $\endgroup$
    – user26290
    Sep 12, 2016 at 14:57
  • $\begingroup$ The paper that I linked to outlines how the E-values are calculated and it also provides an explanation for why they used this approach. $\endgroup$
    – Michael_A
    Sep 13, 2016 at 2:02

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