Many strong Pfam hits are excluded from the display. I need to know the exclusion criteria for that so I can replicate them.
I am guessing (have vague memory) that one criterion is if the name of the protein is in the name of the domain (i.e. we had an algorithm to determine if the domain adds no additional information beyond d the existence of a fungal family). However, I know this cannot be the whole story from looking at the domains on HHyeast pages.
I looked at 20 of the ~1400 Pfam domains from the SGD database which have the gene's names in their own descriptions. Some are included in HHyeast and some are not - I could see no pattern in the few examples I looked at
some domains named after their protein.xlsx
If this makes no sense at all, I'm happy to talk about it!
Tim
Many strong Pfam hits are excluded from the display. I need to know the exclusion criteria for that so I can replicate them.
I am guessing (have vague memory) that one criterion is if the name of the protein is in the name of the domain (i.e. we had an algorithm to determine if the domain adds no additional information beyond d the existence of a fungal family). However, I know this cannot be the whole story from looking at the domains on HHyeast pages.
I looked at 20 of the ~1400 Pfam domains from the SGD database which have the gene's names in their own descriptions. Some are included in HHyeast and some are not - I could see no pattern in the few examples I looked at
some domains named after their protein.xlsx
If this makes no sense at all, I'm happy to talk about it!
Tim