which protein is selected to "represent" protein group

[Gautam Saxena]

In ProteinProphet, what criteria (ie what logic) is used to determine which protein will be chosen to "represent" the protein group in the case that there are multiple protein siblings for the protein group? Similarily, what criteria (is what logic) is used to determine the representative protein among the set of indistinguishable proteins? For example, do we just use the protein with the maximum protein length? Or is it the first protein identified in the FASTA file?

[David Shteynberg]

The proteins in a protein group should be ordered by probability. There is no restriction on ordering of indistinguishable proteins.  I think the current ProteinProphet display simply lists them alphabetically, although the ordering of them within the prot.xml file may be different.

-David

On Tue, Oct 16, 2012 at 7:31 AM, Gautam Saxena <gsaxe...@gmail.com> wrote:

In ProteinProphet, what criteria (ie what logic) is used to determine which protein will be chosen to "represent" the protein group in the case that there are multiple protein siblings for the protein group? Similarily, what criteria (is what logic) is used to determine the representative protein among the set of indistinguishable proteins? For example, do we just use the protein with the maximum protein length? Or is it the first protein identified in the FASTA file?

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