Indels at protein level

[pgaudet]

Hi,

I'd like to have terms to represent indels at the protein level (or please indicate what we should be using). Right now at the transcript level there are: -- conservative_inframe_insertion -- disruptive_inframe_insertion -- conservative_inframe_deletion -- disruptive_inframe_deletion The "conservative" terms do have corresponding polypeptides effects: amino_acid_insertion and amino_acid_deletion

But there are no polypeptide effects that correspond to the 'disruptive' versions. There needs to be indel and frameshifts. Also, if you want a correspondence between the transcript effect and the effect on the polypeptide, you may want to describe 'indel with gain of amino acids' and 'indel with loss of amino acids' (I am not sure what the best formulation may be !)

Thanks,

Pascale

[keilbeck]

Hi Pascal, Let me try to walk thru this with examples. (I don't like to use indeed to describe changes at anything but the DNA level. In SO we separate out the alteration from the effect.)

conservative_inframe_insertion : An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons. --> So the insertion adds codons in frame and the sequence . If I insert CCC into the following seq AAATTTGGG it might look like AAACCCTTTGGG The protein equivalent of this is that the protein is elongated internally by an amino acid. SO term: elongated_polypeptide, but we could specialize to conservative_elongated_polypeptide

disruptive_inframe_insertion : An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon. If I insert CCC into the following seq AAATTTGGG it might look like AACCCATTTGGG so the frame for the protein remains but the first codon is disrupted. The protein equivalent of this is that the protein is elongated and two amino acids have changed. There is no term to describe this currently. disruptive_elongated_polypeptide may be what we need here.

conservative_inframe_deletion AAATTTGGG --> AAAGGG The equivalent polypeptide term in SO is polypeptide_truncation, but again we could add a better term conservative_polypeptide_truncation

-disruptive_inframe_deletion AATGGG Add term disruptive_polypeptide_truncation

Does this capture what you need? Thanks --Karen

[pgaudet]

Hi Karen,

Thanks for looking into this. Your proposal "disruptive_polypeptide_truncation". We also need "disruptive_polypeptide_insertion".

I wonder if it's possible to add 'indel' as a related synonym to all these, so that they can be more easily found ?

Thanks,

Pascale

[pgaudet]

Hi again Karen,

Looking at this once more, in the proposal above, 'disruptive_polypeptide_truncation' should be replaced by 'disruptive_polypeptide_deletion'.

To summarize:

• disruptive_polypeptide_deletion
• disruptive_polypeptide_insertion (disruptive_polypeptide_truncation may still be relevant, we just don't have any examples; those would probably be frameshifts).

Thanks, Pascale