SEA-PHAGES | SIF HHPred Notation

SIF HHPred Notation

Link to this post \| posted 29 Apr, 2020 20:34
EWisner	This question actually relates to all SIF documentation, not just HHPred. Let's say you have good evidence that something is a capsid maturation protease, but you don't get a good HHPred hit. And based on all of the evidence you have, you call it a "capsid maturation protease", how do you then document the SIF-HHPred information? Would it be: SIF-HHPred: NKF - No matches with other 90% probability SIF-HHPred: No matches with other 90% probability SIF-HHPred: capsid maturation protease - No matches with other 90% probability I guess my more general question is with SIF, even if the piece of information doesn't support your call, how to you list it. Thanks! Ellen

Link to this post | posted 29 Apr, 2020 20:34

This question actually relates to all SIF documentation, not just HHPred. Let's say you have good evidence that something is a capsid maturation protease, but you don't get a good HHPred hit. And based on all of the evidence you have, you call it a "capsid maturation protease", how do you then document the SIF-HHPred information?

Would it be:
SIF-HHPred: NKF - No matches with other 90% probability
SIF-HHPred: No matches with other 90% probability
SIF-HHPred: capsid maturation protease - No matches with other 90% probability

I guess my more general question is with SIF, even if the piece of information doesn't support your call, how to you list it.

Thanks!
Ellen

Link to this post \| posted 01 May, 2020 20:16
debbie	Ellen, Historically, we called the capsid maturation protease based on synteny. We would like to have more evidence than that when calling it now. So it depends on which gene and phage genome you are talking about. However, to answer you question generally, if you have the evidence you describe above, you would record exactly what you said for the SIFs, and the function call would be Hypothetical Protein. If you let me know what gene/genome, i could be of greater help. debbie

Link to this post | posted 01 May, 2020 20:16

debbie

Ellen,
Historically, we called the capsid maturation protease based on synteny. We would like to have more evidence than that when calling it now. So it depends on which gene and phage genome you are talking about.

However, to answer you question generally, if you have the evidence you describe above, you would record exactly what you said for the SIFs, and the function call would be Hypothetical Protein. If you let me know what gene/genome, i could be of greater help.

debbie

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SIF HHPred Notation